CRAM files, which are more dense than BAM files, use an additional external
"reference sequence" file to both compress and decompress the read
information. For CRAM tracks to load there is an expectation that the checksum
of the reference sequence used to create the CRAM will be in the CRAM header and
be accessible from the EBI CRAM reference registry or in a designated
"refUrl" location.
Click here to load an example CRAM file from the 1000 Genomes
Project where reads are displayed as a bar graph using the "Display data as
a density graph" option. Loading CRAM tracks is identical to loading BAM files,
the only difference is that instead of providing the URL to a BAM file, the URL
instead points to a CRAM file. Both use type bam in hub and custom track lines,
and both expect an associated index file (CRAM.crai for CRAMs).
Thanks to Jonathan Casper and Brian Raney for the implementation of this feature.
30 June 2016 - Updated Gene Tracks Available for
the Human (hg38) and Mouse (mm10) Assemblies
We are pleased to announce the release of an updated GENCODE Genes
track for the Human (GRCh38/hg38) assembly.
The GENCODE v24 gene set has 197,782 total transcripts, compared with
195,178 in the previous version.
The total number of canonical genes has increased from 49,534 to 49,948.
Comparing the new gene set with the previous version:
193,647 transcripts did not change.
128 transcripts were not carried forward to the new version.
997 transcripts are "compatible" with those in the previous set,
meaning that the two transcripts show consistent splicing. In most cases,
the old and new transcripts differ in the lengths of their UTRs.
406 transcripts overlap with those in the previous set, but do not
show consistent splicing (i.e., they contain overlapping introns with
differing splice sites)
Many thanks to Brian Raney and Luvina Guruvadoo for their work on this track!
---
We are pleased to announce the release of an updated UCSC Genes track for the
Mouse (GRCm38/mm10) assembly.
The new release has 63,759 total transcripts, compared with 63,244
in the previous version. The total number of canonical genes has increased from 32,958
to 33,079. Comparing the new gene set with the previous version:
60,827 transcripts did not change between versions.
148 transcripts were not carried forward to the new version.
1,929 transcripts are "compatible" with those in the previous set, meaning
that the two transcripts show consistent splicing. In most cases, the old and new
transcripts differ in the lengths of their UTRs.
340 transcripts overlap with those in the previous set, but do not show consistent
splicing (i.e., they contain overlapping introns with differing splice sites).
Many thanks to Jonathan Casper and Christopher Lee for their work on this track!
28 June 2016 - New Way to Share Sessions - Public Sessions!
We are excited to announce the release of the
Public Sessions
page, the newest way to share your UCSC Genome Browser snapshots with your colleagues
and the world. The Public Sessions page collects sessions that users have elected to share
publicly. Sessions on this page can be filtered based on assembly, name, or a phrase from
the description. Sessions can also be sorted based on their popularity or creation date.
To add your own sessions to this Public Sessions page, just check the box under "post in
public listing" on the session management page.
The Genome Browser session management page has also received an
update with the release of the new Public Sessions page. Sessions are now arranged in a table,
where varying numbers of sessions can be displayed on a page of this table. Sessions can now be
filtered and ordered based on session name, primary assembly, and creation date. Clicking on the
session name now displays that session in the Genome Browser. Session details, such as the name
or the description, can be changed using the "details" button in the new table layout.
The release of the new Public Sessions page also marks a change in our session expiration policy.
We no longer expire sessions and associated custom tracks four months after their last use.
Please note, however, that the UCSC Genome Browser is not a data storage service and that we
encourage you to keep local copies of your session contents and custom track data.
Thanks to Jonathan Casper and Matthew Speir for their work on this new tool.
15 June 2016 - New Official Asian Mirror Released
We are pleased to announce the introduction of a new supported Genome Browser mirror
to serve our users in Asia. The genome-asia server
(http://genome-asia.ucsc.edu),
which is administered by UCSC, is physically located at the
RIKEN Yokohama Campus
in Japan.
Genome-asia is intended as an alternate, faster access point for those Browser users
who are geographically closer to Asia than to the western United States. The mirror
is functionally identical to the U.S.-based server, with one exception. Custom tracks
residing on the U.S. server are not automatically accessible from the genome-asia mirror;
therefore, the use of these custom tracks and saved sessions containing them will require
some manual intervention.
Genome Browser users located in Asia will be automatically redirected to genome-asia
when they click the "Genomes" menu item on the Genome Browser home page, but will have
the option to remain on the U.S.-based server. In addition to the
genome-asia mirror, we continue to support a Europe-based Genome Browser mirror
(http://genome-euro.ucsc.edu)
in Bielefeld, Germany. A third-party mirror in
Aarhus, Denmark,
is available as an emergency backup in the rare event
that our three supported sites are offline.
We wish to express our special thanks to Dr. Hideya Kawaji at the
RIKEN Advanced
Center for Computing and Communication for making this possible. We would also
like to acknowledge the following members of the UCSC Genome Browser team for their efforts:
Galt Barber, Robert Kuhn, Jorge Garcia, and Luvina Guruvadoo.
6 June 2016 - New video: Exon-only mode
We are pleased to announce the release to our YouTube channel of a new
training video,
in which we demonstrate the recently released Multi-Region feature in
exon-only mode. This feature is useful for those studying gene expression or
undertaking whole-exome sequencing. By removing intronic and intergenic regions,
exon-only mode shows the portion (sometimes as little as a few percent) of the
genome most useful for these analyses.
This video is
indexed
to allow easy access to relevant sections and comes with a transcript for the
hard-of-hearing.
Thanks to Robert Kuhn and David Gibson for production.
To turn on the feature click into the track controls for certain track types,
such as a BAM custom track, and check the box next to "Display data as a
density graph" to see graph configurations and then click "Submit".
To see the new density graph feature in use, please see this example
session.
Thanks to Brian Raney for the implementation of this feature.
10 May 2016 - New Gateway Page!
The UCSC Genome Browser team is proud to announce a newly redesigned
Genome Browser Gateway page.
The Gateway retains its original functionality as a central access point for all genome assemblies
available on our site, while sporting several helpful new features and updates:
Autocomplete searching for any genome browser, genome version, or public hub
Species browsing through a scrollable visual
"tree" menu based on phylogenetic order
Quick access shortcuts to popular browsers
New style and color scheme
Please see our Gateway video for an introduction to these new features.
The new Gateway addresses the need for streamlined access to the rapidly
growing number of genome assemblies available on our public site.
As an alternative to scrolling through long drop-down menus of genome assemblies, you can
now simply type in assembly search terms for autocomplete recognition, visually scroll
through our collection, or click a button to access our most popular species.
Note that a few browser utilities that were previously accessed through links and buttons on the
Gateway page have been moved to the top menu bar:
Browser reset: Genome Browser > Reset All User Settings
Track search: Genome Browser > Track Search
Add custom tracks: My Data > Custom Tracks
Track hubs: My Data > Track Hubs
Configure tracks and display: Genome Browser > Configure
We would like to acknowledge the following people for their contributions
to the new Gateway: original art by Jeff West Design, concept by Robert Kuhn,
software design by Angie Hinrichs, and quality assurance by Cath Tyner.
22 Apr 2016
- Data from the Lens PatSeq Database Now Available
We are pleased to announce the release of a set of tracks showing the genomic mapping of
biomedical sequences submitted as part of patent application documents worldwide. The sequence
data, mappings and associated patent information were obtained from the
PatSeq database provided by
The Lens. The PatSeq data are
mapped to the genome, and the individual sequence features within the tracks are then
color-coded to indicate their status within the associated patent documents.
Track details pages show information about the patent documents in which the sequences
are referenced, and provide a link to The Lens PatSeq Analyzer tool for the given chromosome
range. The PatSeq data are divided into two tracks: a bulk patent track for sequences affiliated
with patents in which more than 100 sequences were submitted, and a non-bulk patent track
for all other sequences. These tracks are currently present on the human (hg19), mouse (mm10),
and Ebola virus (eboVir3) genomes.
Thanks to our collaborators at The Lens, Osmat Jefferson and Deniz Koellhofer, for providing the
data and feedback on the visualization. Thank you to Max Haeussler and Matthew Speir, members of
the UCSC Genome Browser team, for their efforts in creating these tracks.
20 April 2016
- New GTEx Gene Expression Track for hg19 and hg38
We are excited to announce the release of a new gene expression track based on data from the NIH
Genotype-Tissue
Expression (GTEx) project.
This track displays tissue-specific gene expression based on RNA-seq in 53 tissues from 570
donors obtained from the GTEx 'midpoint' data release (V6, October 2015).
The original data for this
track can be found at the GTEX Portal
hosted by the Broad Institute.
This track also features a new gene expression display method that extends the traditional Genome
Browser display — a horizontal bar graph. Every gene is annotated by a graph with colored
bars, each of which corresponds to a specific tissue assayed by the GTEx project. Within
a graph, the bar color indicates the tissue type, using GTEx conventions, and the bar height
depicts the median expression level (in RPKM).
To quickly view the tissue and expression level represented by a bar in the tracks display,
mouse over the bar in the graph.
The complete tissue color legend is shown on the
track configuration page,
and can also be popped up for viewing alongside the track using the right-click menu.
Below the bar graph, a line is shown indicating the gene extent that was used to generate the
annotation, colored by gene class using GENCODE conventions
(e.g. blue for protein-coding,
green for non-coding).
User alert: In the figure above, do you notice how the bar graph sometimes extends past the
righthand end of the associated gene annotation? This is because all bar graphs in the
display are the same width (and have the same tissue ordering) to facilitate comparison.
For example, in this figure (which may also be viewed
here),
the three tall bars in the annotation of the TCAP gene indicate this entire gene is
highly expressed in cardiac and skeletal muscle. It does not indicate that there are
expression peaks in the intergenic region beyond the gene!
Similar to other Genome Browser track displays, clicking on the graph will bring up a description
page that shows a detailed box-and-whiskers plot of
the RPKM data, as well as a description of the methods used to generate the data.
Credit goes to Kate Rosenbloom and Christopher Lee for the implementation and testing of this
feature.
15 April 2016 -
dbSNP 146 Available for hg19 and hg38
We are pleased to announce the release of four tracks derived
from NCBI
dbSNP Build 146 data, available on the two most
recent human assemblies GRCh37/hg19 and GRCh38/hg38.
NCBI's dbSNP database is a collection of "simple nucleotide
polymorphisms" (SNPs), which are a class of genetic variations
that include single nucleotide polymorphisms and small
insertions/deletions (indels). This immense database contains over
150 million such SNPs that cover the human genome.
There are four SNP tracks available as part of this release.
One is a track containing all mappings of reference SNPs
to the human assembly, labeled "All SNPs (146)".
The other three tracks are subsets of this track
and show interesting and easily defined subsets of dbSNP:
Common SNPs (146): uniquely mapped variants that appear
in at least 1% of the population or are 100% non-reference.
Flagged SNPs (146): uniquely mapped variants, excluding
Common SNPs, that have been flagged by dbSNP as
"clinically associated".
Mult. SNPs (146): variants that have been mapped to more
than one genomic location. This track has been shrinking over
the course of the last few releases as dbSNP now excludes most
SNPs whose flanking sequences map to multiple locations in
the genome.
By default, only the Common SNPs (146) are visible;
other tracks must be made visible using the track controls.
You will find the other SNPs (146) tracks on both
of GRCh37/hg19 and GRCh38/hg38 browsers in the "Variation" group.
The tracks were produced at UCSC by Angie Hinrichs and
Matthew Speir. We'd like to thank the dbSNP group at
NCBI for providing access to these data.
15 April 2016 -
Three New Assemblies Now Available in the Genome Browser
A Genome Browser is now available for the gorilla (Gorilla gorilla gorilla)
assembly released December 2014 by the Wellcome Trust Sanger Institute.
For more information and statistics about this assembly, see the NCBI assembly record
for gorGor4.
There are 25 complete chromosomes alongside 40,667 scaffolds with a total size of
3,063,362,754 bases.
Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
FTP server or the
Downloads page.
Please observe the conditions for use when
accessing and using these data sets. The annotation tracks for this browser were
generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the
organizations and individuals who contributed to this release.
- - -
A Genome Browser is now available for the rhesus monkey (Macaca mulatta)
assembly released November 2015 by the
Baylor College of Medicine Human Genome Sequencing Center.
For more information and statistics about this assembly, see the NCBI assembly record
for Mmul_8.0.1.
There are 23 complete chromosomes alongside 284,705 scaffolds with a total size of
3,236,224,332 bases.
Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
FTP server or the
Downloads page.
Please observe the conditions for use when
accessing and using these data sets. The annotation tracks for this browser were
generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the
organizations and individuals who contributed to this release.
- - -
A Genome Browser is now available for the crab-eating macaque (Macaca fascicularis)
assembly released June 2013 by the
Genome Sequencing Center at Washington University, St. Louis.
For more information about this assembly, see
Macaca_fascicularis_5.0 in the NCBI Assembly database. There are
22 complete chromosomes alongside 7,579 scaffolds with a total size of 2,946,843,737 bases.
Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
FTP server or the
Downloads page.
Please observe the conditions for use when
accessing and using these data sets. The annotation tracks for this browser were
generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the
organizations and individuals who contributed to this release.
4 Apr 2016
- New video shows how to obtain sequence or coordinates for exons.
We have released a new video to our YouTube channel. This newest installment in our effort
to share the capabilities of the Genome Browser shows how to
use the Table Browser to obtain either the sequences or the coordinates for
exons in the genes from a chosen region of the genome.
We also want to take this opportuinty to remind you that we offer
on-site workshops to help you and your colleagues make the most out
of the Genome Browser.
1 Apr 2016
- Going Back to Our Roots
For many years, the UCSC Genome Browser has provided a dynamic, cutting-edge interface for
viewing genomic data. As time has gone by, however, it has become clear to us that we
cannot keep this up. It is not fair to you, our users, that our interface keeps changing,
and it has increasingly been a burden on us to keep up with emerging web technologies. Today
that all changes, as we return you to the roots of the web: ASCII.
We apologize again for subjecting you to so many changes over the years, and hope that this
new, more consistent interface will find your approval.
In related news, we have also revised the interface for uploading custom tracks. Rather than
forcing you to wrestle with inconvenient file formats for your data or attempt to set up a web server,
we now provide the option of loading your data from a deck of ISO 6586:1980 punch cards. Simply
punch your data onto a deck and mail the deck to us. Our staff of highly trained specialists
will take care of loading track, and will inform you by mail when the process is complete. Please
note that our current policy of expiring unused custom tracks remains in effect; you must visit
your track within 72 hours of the postmark date. Regrettably, decks cannot be returned.
Card decks may be addressed to:
UCSC Genome Informatics Group
Center for Biomolecular Science & Engineering
CBSE, 501D Engineering II Building
University of California, Santa Cruz
1156 High Street
Santa Cruz, CA 95064
This new file format is also an option for data output from the UCSC Table Browser.
Simply select "mail card deck" from the "output format" menu, and then enter your name and address on the subsequent
page. Please allow 4-6 weeks for delivery.
21 Mar 2016
- Genome Browsers for C. elegans and Brown Kiwi Now Available
A Genome Browser is now available for the Caenorhabditis elegans
assembly released February 2013 by the C. elegans Sequencing Consortium
(C. elegans Sequencing Consortium version WBcel235, UCSC version ce11).
For more information and statistics about this assembly, see the NCBI assembly record
for WBcel235.
There are 7 complete chromosomes with a total size of 100,286,401 bases.
Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
FTP server or the
Downloads page.
Please observe the conditions for use when
accessing and using these data sets. The annotation tracks for this browser were
generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the
organizations and individuals who contributed to this release.
---
A Genome Browser is now available for the brown kiwi (Apteryx australis)
assembly released June 2015 by the
Max-Plank Institute for Evolutionary Anthropology (MPI-EVA version AptMan0,
UCSC version aptMan1). For more information and statistics about this assembly, see
AptMant0 in the NCBI Assembly database. There are
24,719 scaffolds with a total size of 1,523,986,457 bases.
Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
FTP server or the
Downloads page.
Please observe the conditions for use when
accessing and using these data sets. The annotation tracks for this browser were
generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the
organizations and individuals who contributed to this release.
8 Mar 2016
- Combine Multiple Regions of the Genome Browser into a Single Visualization!
Have you ever wished you could remove all of the intronic or intergenic regions from the
Genome Browser display? Have you ever dreamed of being able to visualize multiple
far-flung regions of a genome? Well, now you can with the new "multi-region" option
in the Genome Browser!
The multi-region modes provide four different ways to manipulate the display.
First, we have an "exon-only" mode that allows you to
remove all of the intergenic and intronic sequences from the display, leaving you with
only the exonic regions. Next, there is the "gene-only" mode allowing you to remove only
the intergenic regions from the display, leaving the genes with exons and introns intact.
Then there is the "custom regions" mode that allows you to use a remote BED file to
specify the regions you are interested in viewing alongside each other. Lastly, for human
assemblies hg17 and newer, there is the "alternative haplotype" mode that allows you to
view a haplotype sequence inserted into its position in the reference genome.
To access these exciting, new multi-region modes, first select your organism and assembly
of interest and navigate to the Genome Browser visualization. Below the tracks display,
there is a button labeled "multi-region". Clicking this button will bring up
a configuration box for the different multi-region modes. For example:
From this pop-up, you will be able to switch between the different modes or exit these
multi-region modes if desired. For instance:
Additionally, you can enter the "Exon-only" mode by typing the keyboard shortcut
"e" then "v". You can exit any of the multi-region modes and return to the
default Genome Browser display by typing the keyboard shortcut "d" then "v".
For more information about each individual multi-region mode, please see the
User Guide.
Thank you to Galt Barber, Matthew Speir, and the entire UCSC Genome Browser quality assurance team for
all of their efforts in creating these exciting new display modes.
10 February 2016 -
Two New Assemblies Now Available in the Genome Browser
A Genome Browser is now available for the mouse lemur (Microcebus murinus)
assembly released May 2015 by the
The Broad Institute and the
Baylor College of Medicine Human Genome Sequencing Center.
For more information and statistics about this assembly, see the NCBI assembly record
for Mmur_2.0.
There are 10,311 scaffolds with a total size of 2,438,804,424 bases.
Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
FTP server or the
Downloads page.
Please observe the conditions for use when
accessing and using these data sets. The annotation tracks for this browser were
generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the
organizations and individuals who contributed to this release.
Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
FTP server or the
Downloads page.
Please observe the conditions for use when
accessing and using these data sets. The annotation tracks for this browser were
generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the
organizations and individuals who contributed to this release.
20 Jan 2016
- dbSNP 142 Available for mm10
Data from dbSNP build 142 is now available for the most recent mouse
assembly (mm10/GRCm38). As was the case for previous annotations
based on dbSNP data, there are three tracks in this release.
One is a track containing all mappings of reference SNPs to the
mouse assembly, labeled "All SNPs (142)". The other two tracks
are subsets of this track and show different interesting and
easily defined subsets of dbSNP:
Common SNPs (142): uniquely mapped variants that appear in
at least 1% of the population
Mult. SNPs (142): variants that have been mapped to more
than one genomic location
By default, only the Common SNPs (142) are visible. The other
tracks can be made visible using the track controls.
These three SNPs (142) tracks can be found on the Mouse Dec.
2011 (mm10/GRCm38) browser in the "Variation and Repeats" group.
Thank you to the
dbSNP group at NCBI for making these data publicly available.
The tracks were produced at UCSC by Brian Raney, Angie Hinrichs
and Matthew Speir.
08 January 2016 -
dbSNP 144 Available for hg19 and hg38
We are pleased to announce the release of four tracks derived
from NCBI
dbSNP Build 144 data, available on the two most
recent human assemblies GRCh37/hg19 and GRCh38/hg38.
There are four SNP tracks available as part of this release.
One is a track containing all mappings of reference SNPs
to the human assembly, labeled "All SNPs (144)".
The other three tracks are subsets of this track
and show interesting and easily defined subsets of dbSNP:
Common SNPs (144): uniquely mapped variants that appear
in at least 1% of the population or are 100% non-reference
Flagged SNPs (144): uniquely mapped variants, excluding
Common SNPs, that have been flagged by dbSNP as
"clinically associated"
Mult. SNPs (144): variants that have been mapped to more
than one genomic location
By default, only the Common SNPs (144) are visible;
other tracks must be made visible using the track controls.
You will find the other SNPs (144) tracks on both
of GRCh37/hg19 and GRCh38/hg38 browsers in the "Variation" group.
The tracks were produced at UCSC by Angie Hinrichs and
Luvina Guruvadoo. We'd like to thank the dbSNP group at
NCBI for providing access to these data.
21 December 2015 -
Two New Assemblies Now Available in the Genome Browser
A Genome Browser is now available for the frog (Xenopus tropicalis)
assembly released September 2012 by the US DOE Joint Genome Institute (JGI-PGF)
(JGI v7.0, UCSC version xenTro7). For more
information and statistics about this assembly, see the NCBI assembly record
for
Xtropicalis_v7. There are 7,728 scaffolds with a total size of 1,437,530,879
bases.
Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
FTP server or the
Downloads page.
Please observe the conditions for use when
accessing and using these data sets. The annotation tracks for this browser were
generated by UCSC and collaborators woldwide. See the Credits page for a detailed list of the
organizations and individuals who contributed to this release.
---
A Genome Browser is now available for the cat (Felis catus)
assembly released November 2014 by the International Cat Genome Sequencing Consortium
(ICGSC version Felis_catus_8.0, UCSC version felCat8). For more
information and statistics about this assembly, see the NCBI assembly record
for
Felis_catus_8.0. There are 267,625 scaffolds with a total size of 2,641,342,258
bases.
Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
FTP server or the
Downloads page.
Please observe the conditions for use when
accessing and using these data sets. The annotation tracks for this browser were
generated by UCSC and collaborators woldwide. See the Credits page for a detailed list of the
organizations and individuals who contributed to this release.
16 December 2015 —
Output from Related Tables Now Available in the Data Integrator
In the UCSC Genome Browser database, detailed information on the annotations for many tracks
is stored in extra tables. This information can include things such as identifiers
in other databases, transcript status, or other descriptive information. You can now obtain
data from these related tables in your output from the
Data Integrator.
To add related tables to your Data Integrator output, first, select and add at least one
track to your data sources. Then, scroll down to the "Output Options" section and click the
button.
Lastly, at the bottom of the section for each selected track, you will see a drop-down menu
labeled "Related tables" which allows you to select and add various tables to your output.
For more information about using the Data Integrator, please see the
User Guide.
Thank you to Angie Hinrichs and Matthew Speir for their work on this feature.
9 December 2015 —
Data from 1000 Genomes Project Phase 3 Now Available!
We have made data from Phase 3 of the
1000 Genomes Project
available for the hg19 version of the human assembly.
The data includes almost 90 million variants in the form of single nucleotide variants (SNVs),
insertions/deletions (InDels), and structural variants (SVs). Each variant includes a
detail page that incorporates links to the variant in the dbSNP database, quality scores,
and allele frequency information for various populations. More information is available
on the track description page.
In addition to variant calls, the data includes two tracks that highlight regions of the
genome that are accessible to next generation sequencing technologies that utilize
paired-end reads. One track contains regions that meet the 1000 Genomes Project
"pilot" criteria while the other contains regions that meet a more
"strict" set of guidelines. More information about how these accessible regions
were identified can be found on the
track description page.
Thank you to the 1000 Genomes Project and Tom Blackwell and Mary Kate Wing at the
University of Michigan for making these data available. Thank you to Angie Hinrichs
and Matthew Speir at UCSC for their work on these tracks.
25 November 2015 —
New "View - In External Tools" Menu Sends Data to Prediction Websites!
Do you often get the current sequence with "View - DNA" just to copy
and paste it into another website? With the new menu "View - In External Tools"
you can now send the current region to remote tools with two clicks.
For example, when browsing hg38 and zoomed in on the start of a gene like ABO at
chr9:133,255,000-133,255,555,
click the View menu and select "In External Tools",
or simply type the keyboard shortcut "s" then "t",
to send the region to a list of different prediction tools.
Some of the available tools (not available for all assemblies or all zoom levels)
are primer design and restriction enzyme predictions (Primer3Plus, Primer-BLAST,
NEBCutter), mRNA and protein predictions (RegRNA 2, Riboswitches, RNAfold, PFAM),
cis-regulatory predictions (Promoter 2, RSAT Metazoa), and CRISPR/Cas9 predictions
(CRISPOR, CHOPCHOP), as well as links to view the region at NCBI or Ensembl.
You can suggest other tools via our
Suggestion Box.
Credit goes to Max Haeussler for implementing this new feature.
3 November 2015 —
We are pleased to announce new quick links for the Browser's top menu bar!
The "Genomes" menu now features direct links to jump to browsing the human (hg38 and hg19)
and mouse (mm10 and mm9) assemblies! These links also preserve location information, such
as a favorite gene's location, allowing users to quickly compare available annotation
tracks between two assemblies.
The "Genome Browser" menu now features a "Configure" link to quickly set visibilities for
all tracks on the currently browsed assembly and a "Reset All User Settings" option that will
remove all external hubs and custom tracks data while resetting the entire browser to default
visibilities and the hg38 assembly.
23 September 2015 —
New keyboard shortcuts on the Genome Browser!
We are excited to announce the addition of keyboard shortcuts to navigate
the Genome Browser display! It's now possible to zoom in and out, navigate left
and right, hide all tracks, configure the browser display and much more using
only your keyboard. Use the "?" key to view the entire list of shortcuts.
Happy browsing!
Credit goes to Max Haeussler for implementing this new feature.
14 September 2015 —
Human Genome Browser default changed to GRCh38/hg38
In conjunction with the release of the new 100-species Conservation track on the
hg38/GRCh38 human assembly, we have now changed the default human browser on our
website from hg19 to hg38. This should not affect your current browsing sessions;
if you were last looking at the hg19 (or older) browser, the Genome Browser will
continue to display that assembly for you when you start it up. There are circumstances,
however, in which the selected assembly can switch to the newer version. For instance,
the assembly will switch to hg38 if you reset your browser defaults. If you find
yourself in a situation where some of your favorite browser tracks have "disappeared",
you may want to check that you're viewing the right assembly.
We will continue our efforts to expand the annotation track set on the hg38 browser
to include many of the tracks present on previous human assemblies. In cases where
it makes sense, data may be simply "lifted" from hg19 using migration tools.
In many instances, however, we must rely on our data providers to generate new versions
of their data on the latest assembly. We will publish these data sets as they become available.
For a summary of the new features in the GRCh38 assembly, see the
overview we published in March 2014.
10 September 2015 —
100 Species Conservation Track now available on GRCh38/hg38
We are pleased to announce the release of a new Conservation track based on the human
(GRCh38/hg38) assembly. This track shows multiple alignments of 100 vertebrate species and
measurements of evolutionary conservation using two methods (phastCons and phyloP) from the
PHAST package for all species. The multiple alignments were generated using multiz and other
tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline.
Conserved elements identified by phastCons are also displayed in this track. For more
details, visit the
track description page.
We would like to thank Hiram Clawson and Jonathan Casper for their efforts in creating this track.
12 August 2015 —
New blog post: How to share your UCSC screenthoughts
Do you want to save your UCSC Browser screenthoughts, or share them with a colleague,
or make a slide for a talk, or publish them in a paper? Saving the state of your screen
can take two forms: static or dynamic. You can snap and save a picture of the screen,
or you can share a link to an active Genome Browser. We talk about both approaches
here
and discuss some of the advantages and pitfalls of each.
29 June 2015 —
GENCODE Genes Now the Default Gene Set on the Human (GRCh38/hg38) Assembly
In a move towards standardizing on a common gene set within the bioinformatics
community, UCSC has made the decision to adopt the GENCODE set of gene models
as our default gene set on the human genome assembly. Today we have released
the GENCODE v22 comprehensive gene set as our default gene set on human
genome assembly GRCh38 (hg38), replacing the previous default UCSC Genes set
generated by UCSC. To facilitate this transition, the new gene set employs
the same familiar UCSC Genes schema, using nearly all the same table names
and fields that have appeared in earlier versions of the UCSC set.
By default, the browser displays only the transcripts tagged as "basic" by the
GENCODE Consortium. These may be found in the track labeled "GENCODE Basic" in
the Genes and Gene Predictions track group. However, all the transcripts in the
GENCODE comprehensive set are present in the tables, and may be viewed by
adjusting the track configuration settings for the All GENCODE super-track.
The most recent version of the UCSC-generated genes can still be accessed in
the track "Old UCSC Genes".
The new release has 195,178 total transcripts, compared with 104,178 in the
previous version. The total number of canonical genes has increased from
48,424 to 49,534. Comparing the new gene set with the previous version:
9,459 transcripts did not change.
22,088 transcripts were not carried forward to the new version.
43,681 transcripts are "compatible" with those in the previous set,
meaning that the two transcripts show consistent splicing. In most cases,
the old and new transcripts differ in the lengths of their UTRs.
28,950 transcripts overlap with those in the previous set, but do not
show consistent splicing (i.e., they contain overlapping introns with
differing splice sites)
26 June 2015 -
New Bonobo (panPan1) Assembly Now Available in the Genome Browser
We are pleased to announce the release of a Genome Browser for the May 2012
assembly of bonobo, Pan paniscus (Max-Planck Institute panpan1, UCSC
version panPan1). The assembly was provided by the
Max-Planck Institute for Evolutionary Anthropology.
There are 10,867 scaffolds with a total size of 2,869,190,071 bases.
Bulk downloads of the sequence and annotation data are available via the Genome
Browser
FTP server
or the
Downloads
page. These data have
specific conditions for use.
The bonobo (panPan1) browser annotation tracks were generated by UCSC and
collaborators worldwide. See the
Credits page for a detailed
list of the organizations and individuals who contributed to this release.
12 June 2015 - Data Integrator
Have you ever wished that the Table Browser could associate your custom track items
with some other track, while retaining the item names from both? We have released a
new tool that can do just that, and more: the Data Integrator.
Using the Data Integrator you can select up to five tracks, including custom tracks
and hub tracks, and output tab-separated text that contains all the fields from both
the first track and the overlapping items from the other track(s). If you need only
a subset of the fields from your selected tracks, the Data Integrator allows you to
choose which fields to include in the output. You can also query your current Genome
Browser position, search for positions of items such as genes, SNPs, etc. by name,
query over a set of up to 1000 positions, and even retrieve genome-wide data
(subject to data size). The Data Integrator output can be viewed in your web browser
window or downloaded to an optionally gzip-compressed file. Look for "Data Integrator"
in the Genome Browser Tools menu (top blue bar) if you'd like to try it out.
Thanks to Angie Hinrichs and Matthew Speir for all of their work on this feature.
28 May 2015 -
New UCSC Genes Track Released for GRCm38/mm10
We're happy to announce the release of an updated UCSC Genes track for the GRCm38/mm10
mouse Genome Browser. The new release has 63,244 total transcripts, compared with 61,642
in the previous version. The total number of canonical genes has increased from 32,408
to 32,958. Comparing the new gene set with the previous version:
59,119 transcripts did not change between versions.
55 transcripts were not carried forward to the new version.
2,308 transcripts are "compatible" with those in the previous set, meaning
that the two transcripts show consistent splicing. In most cases, the old and new
transcripts differ in the lengths of their UTRs.
160 transcripts overlap with those in the previous set, but do not show consistent
splicing (i.e., they contain overlapping introns with differing splice sites).
Many thanks to Brian Raney and Matthew Speir for their work on this track!
15 May 2015 -
Work for Us! New Job Openings on the UCSC Genome Browser Project
The UCSC Genome Browser project team is looking for two talented people to join our
engineering staff based in Santa Cruz, CA.
The Software Engineer will work with a small engineering team to support and extend
the UCSC Genome Browser database and software, while interfacing with Genome Browser
collaborators and users worldwide. Our engineering work requires solid experience
with C, UNIX and SQL. For application information and more details, see
Job #150568 on the UCSC staff employment page.
The Quality and User Support Analyst will work with a small QA group that interacts closely
with browser software developers and genomics researchers throughout the world. As
a member of the QA team, you will participate in all aspects of quality assurance for
genomics projects staffed by our group and provide technical support for the affiliated
user communities. For application information and more details about the position,
see Job #1505685 on the UCSC staff employment page.
If you'd like to apply for one of these positions, be sure to submit your
application materials by May 25, 2015, for maximum consideration.
08 April 2015 -
bigGenePred Format Now Supported in the Genome Browser
We are pleased to announce that the UCSC Genome Browser now supports data in
bigGenePred format. bigGenePred format stores annotation items that are a linked collection
of exons, much as BED files do, but bigGenePred has additional information
about the coding frames and other gene specific information. bigGenePred files are created
initially
from BED-type files with some extra fields, using the program bedToBigBed with a special
AutoSQL file that defines the fields of the bigGenePred. The resulting bigBed files are in
an indexed binary format. The advantage of these bigBed files is that only portions of the
files needed to display a particular region are transferred to UCSC. So for large data sets,
bigBed is considerably faster than regular BED files.
This new format is available for use in custom tracks and data hubs. For more information
about bigGenePred, please see our
bigGenePred Track Format help page.
02 April 2015 -
New Tarsier (tarSyr2) Assembly Now Available in the Genome Browser
We are pleased to announce the release of a Genome Browser for the September 2013
assembly of tarsier, Tarsius syrichta (WashU Tarsius_syrichta-2.0.1,
UCSC version tarSyr2). The whole genome shotgun assembly was provided by
Washington University.
There are 337,189 scaffolds with a total size of 3,453,864,774 bases.
Bulk downloads of the sequence and annotation data are available via the Genome
Browser
FTP server
or the
Downloads
page. These data have
specific conditions for use.
The tarsier (tarSyr2) browser annotation tracks were generated by UCSC and
collaborators worldwide. See the
Credits page for a detailed
list of the organizations and individuals who contributed to this release.
02 April 2015 - New Training Video!
Going crazy counting amino acids? Learn an easier way to find the codon number in our new
training video. See our
training page, and our
YouTube channel for
details.
01 April 2015 - New GRCz10 Zebrafish Assembly Now Available
The most recent zebrafish assembly -- GRCz10 (UCSC version danRer10, Sep. 2014) -- is now
available in the UCSC Genome Browser. This is the first zebrafish release by the
Genome Reference Consortium, who took over the improvement and
maintenance of the zebrafish genome assembly.
The GRCz10 assembly improves upon Zv9 by utilizing optical mapping and additional meiotic
mapping to fill gaps with new clone sequence and improve the positioning of assembly
components. This has also been supplemented with a new whole genome shotgun assembly
WGS31. The result is an assembly with a sequence length of 1.3 Gb in 26 chromosomes and
1,035 scaffolds. For more details about the GRCz10 assembly, see the
GRCz10 assembly page or the official
GRCz10 announcement.
The danRer10 sequence and annotation data can be downloaded from the UCSC Genome Browser
FTP server or
downloads page.
We'd like to thank the Genome Reference Consortium for providing this assembly. The UCSC
zebrafish Genome Browser was produced by Hiram Clawson, Brian Raney and Steve Heitner. See
the
credits page for a detailed list
of the organizations and individuals who contributed to this release.
20 March 2015 - New Visualization Option for RepeatMasker
We are excited to announce the release of the new RepeatMasker Visualization track for the
hg38 and mm10 assemblies. This new RepeatMasker track displays detailed information that
includes the amount of unaligned repeat sequence and lines joining repeat fragments.
Additionally, repeats are now colored based on their repeat class. This new RepeatMasker
track incorporates a new details page that includes the detailed RepeatMasker output and
the raw alignment used to generate the final repeat annotation. You can read more about
this track on the description page for either
hg38 or
mm10.
This track is the result of a collaboration between the
Institute for Systems Biology
and the UCSC Genome Browser. We would like to thank Robert Hubley, Arian Smit, Hiram
Clawson, and Matthew Speir for their efforts in creating this track.
03 March 2015 - Use UDR for Quick Sizable Downloads
The UCSC Genome Browser is pleased to share a download protocol to use when downloading
large sets of files from our download servers: UDR (UDT Enabled Rsync). UDR utilizes rsync
as the transport mechanism, but sends the data over the UDT protocol, which enables huge
amounts of data to be downloaded efficiently over long distances.
Please note that we now have two identical download servers to better serve your needs. You
can use either one:
Typical TCP-based protocols like http, ftp and rsync have a problem in that the further
away the download source is from you, the slower the speed becomes. Protocols like UDT/UDR
allow for many UDP packets to be sent in batch, thus allowing for much higher transmit speeds
over long distances. UDR will be especially useful for users who are downloading from places
that are far away from California. The US East Coast and the international community
will likely
see much higher download speeds by using UDR rather than rsync, http or ftp.
Getting UDR & Setting it up on your System:
It should be noted that UDR is not written or managed by UCSC, it was written by the
Laboratory for Advanced Computing at the University of Chicago. It has been tested to work
under Linux, FreeBSD and Mac OSX, but may work under other UNIX variants. The source code can
be obtained here, through GitHub:
If you need help building the UDR binaries or have questions about how UDR functions,
please read the documentation on the GitHub page, and if necessary, contact the UDR authors
via the GitHub page. We recommend reading the documentation on the UDR GitHub page to better
understand how UDR works. UDR is written in C++. UDR is Open Source and is released under the
Apache 2.0 License. You must first have rsync installed on your system.
For your convenience, we are offering a binary distribution of UDR for Red Hat Enterprise
Linux 6.x and 7.x
(or variants such as CentOS 6/7 or Scientific Linux 6/7). You'll find the rpm packages
here:
For RHEL 6 we have 32 bit and 64 bit packages, but for RHEL 7 we have dropped the 32 bit
builds and only
offer a 64 bit package. But if you need a 32 bit package for RHEL 7 you can still download
the source and compile it yourself, as is an option for any other Linux OS.
Example of Using UDR to Download ENCODE Data from the UCSC Genome Browser Download
Server(s):
Once you have a working UDR binary, either by building from source or by installing the rpm
(if you are using RHEL 6.x or other variant), you can download files from either of our our
download servers in a very similar fashion to rsync. For example, using rsync, you may want
to download all of the ENCODE information for the mm9 database using the following command:
If you installed the rpm, use the 'man udr' command for more information via the man page;
if you installed from source please refer to the UDR GitHub page for more details on the
capabilities of UDR and how to use it.
Firewall Considerations:
UDR establishes connections on TCP/9000, then transmits the data stream over UDP/9000-9100.
Your institution may need to modify its firewall rules to allow inbound and outbound ports
TCP/9000 and UDP/9000-9100 from either of the two download machines.
If you decide to install and use UDR, we hope that you experience greatly increased download
speeds. If you have difficulties installing UDR on your system, please contact the
Laboratory
for Advanced Computing through their gitHub page: https://github.com/LabAdvComp/UDR.
26 February 2015 - New Training Video!
Ever wondered how to find the tables associated with your favorite Browser track?
Find out how in our new training video. See our
training page, our
YouTube channel, and our
blog for details.
12 February 2015 - Blat Your Assembly Hub
Assembly data hubs, track hubs that allow researchers to annotate genomes that are
not in the UCSC Genome Browser, can now use blat to quickly find DNA and protein
sequences in their unique assemblies.
While running remote blat servers with the gfServer utility, you can now add lines to your
assembly hub's genomes.txt file to inform the Browser where to send blat searches.
Or by downloading and installing a virtual machine Genome Browser In a Box
(GBiB),
you can alternatively locally run gfServers, preinstalled on GBiB, all from your laptop.
For more information see the Assembly Hub Wiki and the new Quick Start Guide to Assembly Hubs.
11 February 2015 -
dbSNP 142 Available for hg19 and hg38
We are pleased to announce the release of four tracks derived from NCBI
dbSNP Build 142
data, available on the two most recent human assemblies GRCh37/hg19 and GRCh38/hg38.
The new tracks contain a substantial amount of additional annotation data not
included in previous dbSNP tracks, with corresponding coloring and filtering options
in the Genome Browser.
There are four SNP tracks available as part of this release. One is a track
containing all mappings of reference SNPs to the human assembly, labeled
"All SNPs (142)". The other three tracks are subsets of this track and show
interesting and easily defined subsets of dbSNP:
Common SNPs (142): uniquely mapped variants that appear in at least 1%
of the population or are 100% non-reference
Flagged SNPs (142): uniquely mapped variants, excluding Common SNPs,
that have been flagged by dbSNP as "clinically associated"
Mult. SNPs (142): variants that have been mapped to more than one genomic location
By default, only the Common SNPs (142) are visible; other tracks must be
made visible using the track controls. You will find the other SNPs (142) tracks on
both of GRCh37/hg19 and GRCh38/hg38 browsers in the "Variation" group.
The tracks were produced at UCSC by Angie Hinrichs and Jonathan Casper. We'd like
to thank the dbSNP group at NCBI for providing access to these data.
As part of this release, we are also retiring the older dbSNP Build 135 and 137
data from display on the GRCh37/hg19 human assembly. Those tracks will still be
available for viewing on our
preview server,
and the associated masked FASTA files will continue to be available on our
download server.
2 February 2015 - Host a Genome Browser Workshop
New timeslots are now available to host a Genome Browser workshop at your institution.
Thanks to the funding support of NHGRI,
we offer hands-on Genome Browser training onsite at your institution, tailored to your
audience's level of expertise.
For more information or to submit a request to host a workshop,
please visit our signup.
23 January 2015 - Genome Browser YouTube Channel
We are pleased to announce the release of the UCSC Genome Browser
YouTube channel.
The channel contains short videos showing how to use the Genome Browser and associated
tools to solve selected problems. The videos were produced by Robert Kuhn and Pauline
Fujita,
with assistance from Luvina Guruvadoo, Jonathan Casper, Matt Speir and the rest of the
Browser staff.
To access and view this hub, navigate to the
Track Hub gateway page and select "CPTAC Hub v1" from the
Public Hubs list.
Please direct any queries to the Fenyo Lab at
info@fenyolab.org.
In addition, we have also released a PeptideAtlas track which displays peptide identifications from the
PeptideAtlas August 2014 (Build 433) Human build. This build, based on
971 samples containing more than 420
million spectra, identified over a million distinct peptides covering
more than 15,000 canonical proteins. To read more about this track,
please see the track description page. Many thanks to Eric Deutsch,
Zhi Sun, and the PeptideAtlas team at the Institute for Systems Biology,
Seattle for providing this data.
Bulk downloads of the sequence and annotation data are available via the Genome
Browser
FTP server
or the
Downloads
page. These data have
specific conditions for use.
The cow browser annotation tracks were generated by UCSC and
collaborators worldwide. See the
Credits page for a detailed
list of the organizations and individuals who contributed to this release.
Bulk downloads of the sequence and annotation data are available via the Genome
Browser
FTP server
or the
Downloads
page. These data have
specific conditions for use.
The D. melanogaster (dm6) browser annotation tracks were generated by UCSC and
collaborators worldwide. See the
Credits page for a detailed
list of the organizations and individuals who contributed to this release.
29 October 2014 -
Genome Browser in a Box (GBiB)
Sometimes you just want to keep your genomics data to yourself. Have you ever
hesitated when uploading your data set into the UCSC Genome Browser? If so,
you'll be happy to know that we have created a stand-alone personal version:
Genome Browser in a Box (GBiB). If you have sensitive genomics data that you
would like to view securely on your own laptop in the context of the UCSC
Genome Browser, GBiB is for you.
GBiB is an easy-to-install personal copy of the Genome Browser that comes
preloaded with the most popular annotation tracks for human. It is highly
configurable — you can access or download other annotation tracks of
interest, or view any of the other 90+ organisms featured in the public
Genome Browser. GBiB runs inside of Oracle's free VirtualBox virtual machine.
It has the same core functionality as the UCSC Genome Browser, but keeps your
data private and local to your own computer.
GBiB is free for non-commercial use by non-profit organizations, academic
institutions, and for personal use. Commercial use requires purchase of a
license with setup fee and annual payment. Download or purchase GBiB in
our secure online store.
You can read more about GBiB on our
blog,
or in the help doc.
20 October 2014 -
dbSNP 141 Available for hg19 and hg38
We are pleased to announce the release of four tracks derived from NCBI
dbSNP Build 141
data, available on the two most recent human assemblies GRCh37/hg19 and GRCh38/hg38.
The new tracks contain additional annotation data not included in previous dbSNP
tracks, with corresponding coloring and filtering options in the Genome Browser.
There are three SNP tracks available for the GRCh37/hg19 assembly. One is a track
containing all mappings of reference SNPs to the human assembly, labeled
"All SNPs (141)". The other two tracks are subsets of this track and show
interesting and easily defined subsets of dbSNP:
Common SNPs (141): uniquely mapped variants that appear in at least 1%
of the population or are 100% non-reference
Flagged SNPs (141): uniquely mapped variants, excluding Common SNPs,
that have been flagged by dbSNP as "clinically associated"
Unlike previous dbSNP releases for GRCh37/hg19, Build 141 does not include
mappings to alternate haplotype sequences. In addition, variants that map to
multiple genomic locations (e.g. to different chromosomes, or more than one
position on the same chromosome) have been removed.
This release also marks the first set of dbSNP data available for the newest
human assembly, GRCh38/hg38. In addition to the three tracks described for
hg19, there is one additional track available for hg38:
Mult. SNPs (141): variants that have been mapped to more than one genomic location
By default, only the Common SNPs (141) are visible; other tracks must be
made visible using the track controls. You will find the other SNPs (141) tracks on
both of GRCh37/hg19 and GRCh38/hg38 browsers in the "Variation" group.
The tracks were produced at UCSC by Angie Hinrichs and Matthew Speir. We'd like
to thank the dbSNP group at NCBI for providing access to these data.
07 October 2014 -
Introducing the UCSC Genome Browser Blog
We're excited to introduce a new
blog that will feature posts by
Genome Browser staff and guests. On the blog we'll be publishing in-depth information about
UCSC Genome Browser features, tools, projects and related topics that we hope people will
find both useful and interesting. We just published our inaugural post written by Jim Kent,
the UCSC Genome Browser Architect and PI, on the
2014 Ebola Epidemic.
If you have a suggestion for a blog post topic, please let us know via our
suggestion box.
30 September 2014 -
Genome Browser and Portal Released for the Ebola Virus
We are excited to announce the release of a Genome Browser and information portal for the
Jun. 2014 assembly of the Ebola virus (UCSC version eboVir3, GenBank accession
KM034562)
submitted by the Broad Institute. We have worked closely with the Pardis Sabeti lab at
the Broad Institute and other Ebola experts throughout the world to incorporate
annotations that will be useful to those studying Ebola. Annotation tracks included in this
initial release include genes from NCBI, B- and T-cell epitopes from the IEDB, structural annotations from UniProt and a wealth of SNP data from the
2014 publication
by the Sabeti lab. This initial release also contains a 160-way alignment
comprising 158 Ebola virus sequences from various African outbreaks and 2 Marburg virus
sequences.
You can find links to the Ebola virus Genome Browser and more information on the Ebola virus
itself on our Ebola Portal page.
Bulk downloads of the sequence and annotation data are available via the Genome
Browser
FTP server
or the
Downloads
page.
The Ebola virus (eboVir3) browser annotation tracks were generated by UCSC and
collaborators worldwide. See the
Credits page for a detailed
list of the organizations and individuals who contributed to this release and
the conditions for use of these data.
23 September 2014 -
Ensembl Regulatory Build Now Available in the Genome Browser
We are pleased to announce that data from the
Ensembl Regulatory Build is now available in the UCSC Genome Browser
as a public track hub for both hg19 and hg38. This track hub contains promoters and their
flanking regions, enhancers, and many other regulatory features predicted across a number
of cell lines using annotated segmentation states. Click
here
to view this hub on the hg19 assembly, or click
here
to view it on the hg38 assembly.
We would like to thank our collaborators Daniel Zerbino, Steve Wilder, and Nathan Johnson
from Ensembl and Kate Rosenbloom and Matthew Speir from UCSC for their efforts in
bringing these resources to the UCSC Genome Browser.
The website for up-to-date information about the ENCODE project is no
longer hosted at genome.ucsc.edu/ENCODE.
Those UCSC ENCODE pages now archive information and tools from the ENCODE
production and pilot phases (2003 to 2012) including live links to visualize and download
data.
Please navigate to the new ENCODE portal for recent data releases. Along with the ability to
use faceted searching to explore all ENCODE data, the ENCODE portal provides visualization
in the UCSC Genome Browser via a "Visualize Data" link on assay pages when
processed data files are available.
03 September 2014 -
Data from the FaceBase Consortium Now Available in the Genome Browser
We are pleased to announce that much of the data from the
FaceBase Consortium is now available in the UCSC Genome Browser as a
public track hub. This track hub contains data from numerous experiments carried out by
the Potter and Visel labs to study craniofacial development in mice and humans, with
tracks for the mm9, mm10, hg18, and hg19 assemblies. You can check out the hub on the
mm9 assembly
here. In addition to this public track hub, we have a set of
microarray expression data hosted as a native track for both the mm9 and mm10 assemblies.
This expression data compares expression across the mouse genome for a number of embryonic
days and craniofacial cell types. For more information on this track, please see the track
description page.
We would like to thank Robert Kuhn, Pauline Fujita, and Matthew Speir from UCSC and Thomas
Maher from the FaceBase Consortium for their efforts in bringing these resources to the
UCSC Genome Browser.
30 July 2014 -
New Rat (rn6) Assembly Now Available in the Genome Browser
We are excited to announce the release of a Genome Browser for the July 2014 assembly
of rat, Rattus norvegicus (RGSC Rnor_6.0, UCSC version rn6)! This
assembly is provided by the Rat Genome Sequencing Consortium, which is comprised of
eight research organizations across the United States and Canada and led by the
Baylor College of Medicine.
The new RGSC Rnor_6.0 assembly contains a new, partially assembled Y chromosome
as well as improvements to other regions of the genome. You can find more information
on the RGSC's efforts to sequence rat genome on the Baylor College of Medicine's
project page.
Bulk downloads of the sequence and annotation data are available via the Genome
Browser
FTP server
or the
Downloads
page. These data have
specific conditions for use.
The rat (rn6) browser annotation tracks were generated by UCSC and
collaborators worldwide. See the
Credits page for a detailed
list of the organizations and individuals who contributed to this release.
15 July 2014 -
New Shrew (sorAra2) Assembly Now Available in the Genome Browser
We are pleased to announce the release of a Genome Browser for the August 2008
assembly of shrew, Sorex araneus (Broad SorAra2.0, UCSC version
sorAra2). The whole genome shotgun assembly was provided by
The Broad Institute.
There are 12,845 scaffolds with a total size of 2,423,158,183 bases.
Bulk downloads of the sequence and annotation data are available via the Genome
Browser
FTP server
or the
Downloads
page. These data have
specific conditions for use.
The shrew (sorAra2) browser annotation tracks were generated by UCSC and
collaborators worldwide. See the
Credits page for a detailed
list of the organizations and individuals who contributed to this release.
15 July 2014 -
New Pika (ochPri3) Assembly Now Available in the Genome Browser
We are pleased to announce the release of a Genome Browser for the May 2012
assembly of pika, Ochotona princeps (Broad OchPri3.0, UCSC version
ochPri3). The whole genome shotgun assembly was provided by
The Broad Institute.
There are 10,420 scaffolds with a total size of 2,229,835,716 bases.
Bulk downloads of the sequence and annotation data are available via the Genome
Browser
FTP server
or the
Downloads
page. These data have
specific conditions for use.
The pika (ochPri3) browser annotation tracks were generated by UCSC and
collaborators worldwide. See the
Credits page for a detailed
list of the organizations and individuals who contributed to this release.
19 June 2014 -
Conservation Track Released for Rat
We are pleased to announce the release of a new Conservation track based on the rat
(RGSC 5.0/rn5) assembly. This track shows multiple alignments of 13 vertebrate species and
measurements of evolutionary conservation using two methods (phastCons and phyloP) from the
PHAST package for all species. The multiple alignments were generated using multiz and other
tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline.
Conserved elements identified by phastCons are also displayed in this track. For more
details, visit the
track description page.
With the release of this new conservation track, we have changed the default rat browser on
our website from rn4 to rn5. In general, the Genome Browser will continue to display
whichever rat assembly you have already been viewing, and will default to the rn5 assembly
only for those users who haven't recently viewed a rat assembly. However, there are
circumstances in which the assembly may update the view to the newer version, for instance
if you reset your browser settings to the default values. If you find yourself
in a situation where some of your favorite browser tracks have "disappeared", you
may want to check that you're viewing the expected assembly.
We would like to thank Pauline Fujita, Matthew Speir, and Hiram Clawson for their efforts in
creating this track.
30 May 2014 -
New Human Variation Track Now Available
We would like to announce the release of the new Exome Variant Server (EVS) Variants track.
The EVS, maintained by the
Nickerson lab at the University
of Washington, contains variant annotations for over 6,500 exomes that were sequenced as
part of the NHLBI GO Exome Sequencing Project (ESP). This annotation includes
information such as function, clinical association, dbSNP rsID, average sample read depth,
and much more. You can find more information on how the data for this track was generated on
the track description page.
We would like to acknowledge Tim Dreszer and Matthew Speir for their hard work in creating
this track.
27 May 2014 -
New Roadmap Epigenomics Integrative Analysis Hub now available
We are pleased to announce the addition of the
Roadmap Epigenomics Integrative Analysis Hub
to our list of publicly available track hubs.
This new hub, produced by VizHub at
Washington University in St. Louis (WUSTL), contains hundreds of tracks that cover the wide
range of epigenomic data available from the Roadmap Epigenomics Project. This hub contains data from over 40
different assays carried out on over 250 different cell and sample types. These assays
include RNA-seq, MeDIP-seq, MRE-seq, methylC-seq, DNase hypersensitivity, chromHMM
segmentation, ChIP-seq, and more than 30 histone modifications. The data contained in this
hub is complementary to the ENCODE data available at UCSC and in the ENCODE Integrative
Analysis public hub.
You can view more data produced by the Roadmap Epigenomics Project in their other publicly
available track hub, the Roadmap Epigenomics Data Complete Collection. You can use these two
hubs together to access all the available Roadmap Epigenomics Project data using the UCSC
Genome Browser. To access and view these hubs, navigate to the
Track Hub gateway page and select both the Roadmap
Epigenomics Integrative Analysis Hub and Roadmap Epigenomics Data Complete Collection Hub
from the Public Hubs list.
Any queries about the data should be directed to
Ting Wang from VizHub.
15 May 2014 -
New UCSC Gene Track Released for GRCh38/hg38
We're happy to announce the release of a new UCSC Genes track for the
GRCh38/hg38 human Genome Browser.
The new release has 104,178 transcripts, compared with 82,960 in the previous
version on hg19. The total number of canonical genes has increased from
31,848 to 48,424. Comparing the new gene set with the previous version:
69,691 transcripts did not change between versions.
619 transcripts were not carried forward to the new version.
8,879 transcripts are "compatible" with those in the previous set,
meaning that the two transcripts show consistent splicing.
3,393 transcripts overlap with those in the previous set.
Many thanks to Brian Raney, Jim Kent, and Luvina Guruvadoo
for their work on this track!
09 May 2014 -
Three New Assemblies Now Available in the Genome Browser
A Genome Browser is now available for the Chinese hamster (Cricetulus griseus)
assembly released July 2013 by the Beijing Genomics Institution-Shenzhen
(BGI version C_griseus_v1.0, UCSC version criGri1). For more
information and statistics about this assembly, see the NCBI assembly record
for
C_griseus_v1.0. There are 52,711 scaffolds with a total size of 2,360,146,428
bases.
Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
FTP server or the
Downloads page.
Please observe the conditions for use when
accessing and using these data sets. The annotation tracks for this browser were
generated by UCSC and collaborators woldwide. See the Credits page for a detailed list of the
organizations and individuals who contributed to this release.
---
A Genome Browser is now available for the hedgehog (Erinaceus europaeus)
assembly released May 2012 by the Broad Institute
(Broad version EriEur2.0, UCSC version eriEur2). For more
information and statistics about this assembly, see the NCBI assembly record
for
EriEur2.0. There are 5,802 scaffolds with a total size of 2,715,720,925
bases.
Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
FTP server or the
Downloads page.
Please observe the conditions for use when
accessing and using these data sets. The annotation tracks for this browser were
generated by UCSC and collaborators woldwide. See the Credits page for a detailed list of the
organizations and individuals who contributed to this release.
---
A Genome Browser is now available for the zebra finch (Taeniopygia guttata)
assembly released February 2013 by The Genome Institute at Washington University
(WUSTL version Taeniopygia_guttata-3.2.4, UCSC version taeGut2). For more
information and statistics about this assembly, see the NCBI assembly record
for
Taeniopygia_guttata-3.2.4. There are 37,096 scaffolds with a total size of 1,232,135,591
bases.
Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
FTP server or the
Downloads page.
Please observe the conditions for use when
accessing and using these data sets. The annotation tracks for this browser were
generated by UCSC and collaborators woldwide. See the Credits page for a detailed list of the
organizations and individuals who contributed to this release.
08 May 2014 -
New Elephant Shark (calMil1) Assembly Now Available in the Genome Browser
A Genome Browser is now available for the elephant shark (Callorhinchus milii)
assembly released December 2013 by the Singapore Institute of Molecular and Cell Biology
(IMCB version Callorhinchus_milii-6.1.3, UCSC version calMil1). For more
information and statistics about this assembly, see the NCBI assembly record
for
Callorhinchus_milii-6.1.3. There are 21,204 scaffolds with a total size of 974,498,586
bases.
Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
FTP server or the
Downloads page.
Please observe the conditions for use when
accessing and using these data sets. The annotation tracks for this browser were
generated by UCSC and collaborators woldwide. See the Credits page for a detailed list of the
organizations and individuals who contributed to this release.
06 May 2014 -
Introducing the new stacked overlay for multi-wiggle tracks
We are excited to announce the release of the new stacked
overlay method for multi-wiggle tracks. This new stacked overlay
method displays each graph stacked on top of each other.
Navigate to the track settings for H3K27Ac Mark on the human hg19 assembly to view this new stacked
overlay method on a multi-wiggle track. On the track settings page,
from the "Overlay method" drop-down menu select "stacked". Make sure
that the display mode is not set to hide, and click submit.
Credit for the implementation and testing of this new feature goes to
Brian Raney and Matthew Speir.
29 April 2014 - 100-species Conservation track re-release
We released the initial version of the 100-species Conservation track
for the hg19 human assembly in November 2013. Over the past few months,
we found a couple of inconsistencies and decided, for the integrity of
the data, that we should rerun the computation pipeline and re-release
the data. The fixes required minimal changes, and resulted in a more
precise data set. We published the new version of the hg19 100-species
Conservation track on 15 April 2014.
Here are more details about the two fixes that we made:
1. We tracked down the cause of some unusual gaps in the alignments to a
bug in the multiz program used in our alignment pipeline. The Penn State
Bioinformatics Group provided us with a fixed version of multiz that we
used to rerun the pipeline.
2. We inadvertently used the pre-release assembly for one of the species
in the 100-way alignment: the panda. We replaced this assembly with the
correct version and verified that the data sets for all other species
were correct before rerunning the pipeline.
18 April 2014 - New Motif Displays for Transcription Factor ChIP-seq Track and New Genome Segmentations from ENCODE
The Browser's default displayed Transcription Factor ChIP-seq track is updating to the
latest data release,
which has been enhanced with the display of Factorbook motifs. Within a cluster, a green
highlight indicates the highest scoring site of a Factorbook-identified canonical motif for
the corresponding factor. Upon clicking a transcription factor's cluster with a motif, the
details page now displays the motif's sequence logo, alignment and underlying Positional
Weight Matrix. Also, the track configuration page now enables the filtering of factors.
The newly added
Genome Segmentations from ENCODE tracks display multivariate genome-segmentation performed on
six human cell types
(GM12878, K562, H1-hESC, HeLa-S3, HepG2, and HUVEC), integrating ChIP-seq data for
eight chromatin marks, RNA Polymerase II, the CTCF transcription factor and input data.
In total, twenty-five states were used to segment the genome, and these states were then
grouped and colored to
highlight predicted functional elements. These Genome Segmentations are the same data as
found in the Analysis Working Group Hub, but are now hosted natively in the Browser with
enhanced filtering capability where desired segmented states can be selected using the
'Filter by Segment Type' control on the track configuration page.
15 April 2014 -
New Minke Whale (balAcu1) Assembly Now Available in the Genome Browser
A Genome Browser is now available for the minke whale (Balaenoptera acutorostrata scammoni)
assembly released October 2013 by the
Korea Ocean Research & Development Institute (KORDI version BalAcu1.0, UCSC version balAcu1).
For more information and statistics about this assembly, see the NCBI assembly record for
BalAcu1.0. There are
10,776 scaffolds with a total size of 2,431,687,698 bases.
Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
FTP server or the
Downloads page. Please
observe the conditions for use when accessing and
using these data sets. The annotation tracks for this browser were generated by UCSC and
collaborators worldwide. See the Credits
page for a detailed list of the organizations and individuals who contributed to this release.
11 April 2014 -
New UCSC Genes Track Released for GRCm38/mm10
We're happy to announce the release of an updated UCSC Genes track for the GRCm38/mm10
mouse Genome Browser. The new release has 61,642 total transcripts, compared with 59,121
in the previous version. The total number of canonical genes has increased from 31,469
to 32,408. Comparing the new gene set with the previous version:
54,714 transcripts did not change between versions.
19 transcripts were not carried forward to the new version.
3,866 transcripts are "compatible" with those in the previous set, meaning
that the two transcripts show consistent splicing. In most cases, the old and new
transcripts differ in the lengths of their UTRs.
522 transcripts overlap with those in the previous set, but do not show consistent
splicing (i.e., they contain overlapping introns with differing splice sites).
Many thanks to Brian Raney and Steve Heitner for their work on this track!
06 March 2014 -
The new GRCh38 Human Genome Browser is here!
In the final days of 2013, the
Genome Reference Consortium (GRC) released the eagerly awaited GRCh38
human genome assembly, the first major revision of the human genome in more than four
years. During the past two months, the UCSC team has been
hard at work building a browser that will let our users explore the new
assembly using their favorite Genome Browser features and tools.
Today we're announcing the release of a preliminary browser on the GRCh38
assembly. Although we still have plenty of work ahead of us in constructing the rich
feature set that our users have come to expect, this early release will allow you to
take a peek at what's new.
Starting with this release, the UCSC Genome Browser version numbers for human
assemblies will match those of the GRC to minimize version confusion. Hence, the GRCh38
assembly is referred to as hg38 in Genome Browser datasets and documentation. We've
also made some slight changes to our chromosome naming scheme that affect primarily the
names of haplotype chromosomes, unplaced contigs and unlocalized contigs. For more details
about this, see the
hg38 gateway page.
What's new in GRCh38?
Alternate sequences - Several human chromosomal regions exhibit sufficient
variability to prevent adequate representation by a single sequence. To address this, the
GRCh38 assembly provides alternate sequence for selected variant regions through the
inclusion of alternate loci scaffolds (or alt loci). Alt loci are
separate accessioned sequences that are aligned to reference chromosomes. This assembly
contains 261 alt loci, many of which are associated with the LRC/KIR area of chr19 and the
MHC region on chr6. (See the
sequences page for a complete list of
the reference chromosomes and alternate sequences in GRCh38.)
Centromere representation - Debuting in this release, the large megabase-sized gaps
that were previously used to represent centromeric regions in human assemblies have been
replaced by sequences from centromere models created by
Karen Miga et al. of UCSC's
Kent lab, under the
guidance and mentorship of the Willard lab at Duke University. The models, which provide the
approximate repeat number and order for each centromere, will be useful for read mapping
and variation studies.
Mitochondrial genome - The mitochondrial reference sequence included in the GRCh38
assembly and hg38 Genome Browser (termed "chrM" in the browser) is the
Revised Cambridge Reference Sequence (rCRS) from
MITOMAP with GenBank accession
number J01415.2 and RefSeq accession number NC_012920.1. This differs from the chrM
sequence (RefSeq accession number NC_001907) used by the previous hg19 Genome Browser,
which was not updated when the GRCh37 assembly later transitioned to the new version.
Sequence updates - Several erroneous bases and misassembled regions in GRCh37 have
been corrected in the GRCh38 assembly, and more than 100 gaps have been filled or reduced.
Much of the data used to improve the reference sequence was obtained from other genome
sequencing and analysis projects, such as the 1000 Genomes Project.
Analysis set - The GRCh38 assembly offers an "analysis set" that was
created to accommodate next generation sequencing read alignment pipelines. Several
GRCh38 regions have been eliminated from this set to improve read mapping.
The analysis set may be downloaded from the Genome Browser
downloads page.
For more information about the files included in the GRCh38 GenBank submission,
see the
GRCh38 README. The GRCh38 GenBank record provides a detailed
array of statistics about this assembly.
Bulk downloads of the sequence and annotation data may be obtained from the Genome
Browser FTP server
or the
Downloads
page. The annotation tracks for this browser were generated by UCSC and collaborators
worldwide.
Much more to come! This initial release of the hg38 Genome Browser provides a
rudimentary set of annotations. Many of our annotations rely on data sets from external
contributors (such as our popular SNPs tracks) or require massive computational effort
(our comparative genomics tracks). In the upcoming months/years, we will release many more
annotation tracks as they become available. To stay abreast of new datasets, join our
genome-announce mailing list or follow us on
twitter.
We'd like to thank our GRC and NCBI collaborators who worked closely with
us in producing the hg38 browser. Their quick responses and helpful feedback were a
key factor in expediting this release. The production of the hg38 Genome Browser was
a team effort, but in particular we'd like to acknowledge the engineering efforts of Hiram
Clawson and Brian Raney, the QA work done by Steve Heitner, project guidance
provided by Ann Zweig, Robert Kuhn, and Jim Kent, and documentation work by Donna
Karolchik.
See the Credits page for a detailed
list of the organizations and individuals who contributed to this release.
04 March 2014 -
Introducing the Genome Browser Highlight Feature
We are excited to announce the new highlight feature in the UCSC
Genome Browser. Using drag-and-select, you can now highlight a
region or gene of interest.
To highlight a region: Click and hold the mouse button on one edge
of the desired area to be highlighted in the Base Position track,
drag the mouse right or left to highlight the selection area, then
release the mouse button. Click the "Highlight" button on the
"drag-and-select" popup. More details about this new feature
can be found on our
help page.
Credit goes to Tim Dreszer, Larry Meyer, Robert Kuhn and Luvina Guruvadoo
for the design, development and testing of this feature. Additional
testing was also provided by several members of the QA team.
28 February 2014 -
New! Expanded onsite workshop program!
Explore the full power of the UCSC Genome Browser! Thanks to the funding support
of NHGRI, we can now offer hands-on Genome Browser training onsite at your
institution, tailored to your audience's level of expertise. Through this
program, the services of our expert trainer are provided for free, and
participating institutions cover only the transportation from UCSC, lodging,
and a flat fee to cover other costs.
For more information or to submit a request for a workshop, please visit
our signup.
22 January 2014 -
All the DNA on the internet now at your fingertips!
We're pleased to announce the release of the Web Sequences track on the UCSC Genome Browser.
This track, produced in collaboration with Microsoft Research, contains the results of a
30-day scan for
DNA sequences from over 40 billion different webpages. The sequences were then mapped with
Blat to
the human genome (hg19) and numerous other species including mouse (mm9), rat (rn4), and
zebrafish
(danRer7). The data were extracted from a variety of sources including patents, online
textbooks,
help forums, and any other webpages that contain DNA sequence. In essence, this track
displays the
Blat alignments of nearly every DNA sequence on the internet! The
Web Sequences
track description page contains more details on how the track was generated.
We would like to acknowledge Max Haeussler and Matt Speir from the UCSC Genome Browser staff
and Bob Davidson from Microsoft Research for their hard work in creating this track.
14 January 2014 -
Two E. coli comparative assembly hubs now available
We're pleased to add two new assembly hubs produced by the UCSC
David Haussler lab
to our collection of publicly available hubs. The new hubs feature over 60 bacterial
assemblies,
including more than 55 different E. coli strains. The assembly annotations include genes,
pathogenic genes, conservation, GC percent, repetitive elements and much more.
These hubs focus on comparative genomics and showcase the new "snake" track type. Snakes,
which visualize alignments from
Hierarchical Alignment
(HAL) files, provide a way to view sets of pairwise gapless alignments that may overlap on
both the chosen genome (reference) and the query genome, and show various types of genomic
variations
such as insertions, substitutions, and duplications. More details about the new snake track
display and its configuration options can be found on our Genome Browser
help
page.
To access and view these hubs, navigate to the
Track Hub gateway page
and select one of the two E. coli comparative assembly hubs from the Public Hubs list.
We would like to acknowledge Ngan Nguyen, Glenn Hickey, Brian Raney, Joel Armstrong,
Benedict Paten, Matt Speir, and Luvina Guruvadoo for their hard work in creating these hubs.
27 November 2013 -
100 Species Conservation Track now available on hg19
After 15.4 years of CPU run-time in 9,905,594 individual 'jobs' and 99 cluster runs for
lastz
pair-wise alignment...we are excited to announce the release of a 100 species alignment on
the hg19/GRCh37 human Genome Browser.
This new Conservation track shows multiple alignments of 100 species and measurements of
evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package.
This adds 40 more species to the existing 60-way on the mm10 mouse browser. For more
information about the 100 species Conservation track, see its
description page.
We'd also like to acknowledge the hard work of the UCSC Genome Browser staff who pulled
together the information for this track: Hiram Clawson and Pauline Fujita.
24 October 2013 -
Job Opening: UCSC Genome Browser Trainer
The Center for Biomolecular Science
and Engineering (CBSE) at University of California Santa Cruz
seeks an articulate, self-motivated educator for the two-year position of UCSC Genome
Browser trainer. The trainer develops curriculum and provides in-person training on the UCSC
Genome Browser at universities, hospitals, institutes, and professional
meetings in the United States and internationally. Typical audiences include graduate
and post-graduate biologists and doctors, with Genome Browser experience ranging from novice
users to bioinformatics specialists. Presentations include formal talks, problem-solving
sessions, and two-day workshops.
This position requires a Master's degree in a biological science, depth in molecular
biology, experience in a research environment, working knowledge of the UCSC Genome Browser,
understanding of its role in research methodology, and experience teaching or training in a
scientific environment. Preferred qualifications include a PhD in a relevant field,
experience with video production, and experience with HTML or web content management
systems.
For more information and to apply for this position, see
Job #1304619 on the UCSC Staff
Employment website.
23 October 2013 -
dbSNP 138 Available for hg19
We are pleased to announce the release of four tracks derived from NCBI
dbSNP Build 138
data, available on the human assembly (GRCh37/hg19).
The new tracks contain additional annotation data not included in previous dbSNP
tracks, with corresponding coloring and filtering options in the Genome Browser.
As was the case for the annotations based on the previous dbSNP build 137, there are
four tracks in this release. One is a track
containing all mappings of reference SNPs to the human assembly, labeled
"All SNPs (138)". The other three tracks are subsets of this track and show
interesting and easily defined subsets of dbSNP:
Common SNPs (138): uniquely mapped variants that appear in at least 1%
of the population or are 100% non-reference
Flagged SNPs (138): uniquely mapped variants, excluding Common SNPs,
that have been flagged by dbSNP as "clinically associated"
Mult. SNPs (138): variants that have been mapped to more than one genomic location
By default, only the Common SNPs (138) are visible; other tracks must be
made visible using the track controls.
You will find the four SNPs (138) tracks on the Human Feb. 2009 (GRCh37/hg19)
browser in the "Variation and Repeats" group.
The tracks were produced at UCSC by Angie Hinrichs and Luvina Guruvadoo. We'd like
to thank the dbSNP group at NCBI for providing access to these data.
11 October 2013 -
Updated DGV Structural Variation Track
The UCSC Genome Browser is pleased to announce an updated DGV Structural Variation
track to reflect the official launch of the new Database of Genomic Variants. The new release includes a number of
updates and corrections and completes DGV's transition from their Beta version as
they retire their original site for the new and improved site. For more background on
DGV's changes, please see DGV's June 2013 newsletter.
26 September 2013 -
New American Alligator (allMis1) Assembly Now Available in the Genome Browser
A Genome Browser is now available for the American alligator
(Alligator mississippiensis) assembly released
August 2012 by the International Crocodilian Genomes Working Group
(version allMis0.2, UCSC version allMis1).
Please note the assembly construction details.
For more information and statistics about this assembly,
see the NCBI assembly record for
allMis0.2. There are 14,645 scaffolds
with a total size of 2,174,259,888 bases.
Bulk downloads of the sequence and annotation data may be obtained from the Genome
Browser FTP server
or the
Downloads
page. Please observe the
conditions for use
when accessing and using these data sets. The annotation tracks for this browser
were generated by UCSC and collaborators worldwide. See the
Credits page for a detailed
list of the organizations and individuals who contributed to this release.
11 September 2013 -
New Alpaca (vicPac2) Assembly Now Available in the Genome Browser
We are pleased to announce the release of a Genome Browser for the March 2013
assembly of alpaca, Vicugna pacos (Broad Vicugna_pacos-2.0.1, UCSC version
vicPac2). The whole genome shotgun assembly was provided by
The Broad Institute.
There are 276,725 scaffolds with a total size of 2,172,191,320 bases.
Bulk downloads of the sequence and annotation data are available via the Genome
Browser
FTP server
or the
Downloads
page. These data have
specific conditions for use.
The alpaca (vicPac2) browser annotation tracks were generated by UCSC and
collaborators worldwide. See the
Credits page for a detailed
list of the organizations and individuals who contributed to this release.
04 September 2013 -
New Tenrec (echTel2) Assembly Now Available in the Genome Browser
We are pleased to announce the release of a Genome Browser for the November 2012
assembly of tenrec, Echinops telfairi (Broad EchTel2.0, UCSC version
echTel2). The whole genome shotgun assembly was provided by
The Broad Institute.
There are 8,402 scaffolds with a total size of 2,947,024,286 bases.
Bulk downloads of the sequence and annotation data are available via the Genome
Browser
FTP server
or the
Downloads
page. These data have
specific conditions for use.
The tenrec (echTel2) browser annotation tracks were generated by UCSC and
collaborators worldwide. See the
Credits page for a detailed
list of the organizations and individuals who contributed to this release.
04 September 2013 -
New Sheep (oviAri3) Assembly Now Available in the Genome Browser
We are pleased to announce the release of a Genome Browser for the August 2012
assembly of sheep, Ovis aries (ISGC Oar_v3.1, UCSC version
oviAri3). The whole genome shotgun assembly was provided by the
International Sheep Genomics Consortium.
There are 5,698 scaffolds with a total size of 2,619,054,388 bases.
Bulk downloads of the sequence and annotation data are available via the Genome
Browser
FTP server
or the
Downloads
page. These data have
specific conditions for use.
The sheep (oviAri3) browser annotation tracks were generated by UCSC and
collaborators worldwide. See the
Credits page for a detailed
list of the organizations and individuals who contributed to this release.
22 August 2013
- Three New Human Variation Tracks Released
The three databases have varying license restrictions. UniProt provides complete
information about the mutation amino acid change, the disease and a link to the
publications that mention it. LOVD provides the mutation and a link to a website
with disease and publication details. HGMD provides some coordinates and a link to
its own website which requires registration.
These tracks are intended for use primarily by physicians and other professionals
concerned with genetic disorders, by genetics researchers, and by advanced students
in science and medicine. While the Genome Browser database is open to the public, users
seeking information about a personal medical or genetic condition are urged to consult
with a qualified physician for diagnosis and for answers to personal questions.
We'd like to thank all three databases for their help in putting the data together. The
tracks were produced at UCSC by Maximilian Haeussler and Steve Heitner.
22 July 2013
- Variant Annotation Integrator
In order to assist researchers in annotating and prioritizing thousands
of variant calls from sequencing projects, we have developed the Variant
Annotation Integrator (VAI). Given a set of variants uploaded as a
custom track (in either pgSnp
or VCF format), the VAI will
return the predicted functional effect (e.g., synonymous, missense,
frameshift, intronic) for each variant. The VAI can optionally add
several other types of relevant information, including: the
dbSNP
identifier if the variant is found in dbSNP, protein damage scores for
missense variants from the Database of Non-synonymous Functional Predictions (dbNSFP),
and conservation scores computed from multi-species alignments. The VAI
also offers filters to help narrow down results to the most interesting
variants.
Future releases of the VAI will include more input/upload options,
output formats, and annotation options, and a way to add information
from any track in the Genome Browser, including custom tracks.
There are two ways to navigate to the VAI: (1) From the "Tools"
menu, follow the "Variant Annotation Integrator" link. (2)
After uploading a custom track, hit the "go to variant annotation
integrator" button. The user's guide is at the bottom of the page,
under "Using the Variant Annotation Integrator."
Thank you to Angie Hinrichs, Bob Kuhn, Brian Raney, Brooke Rhead, and
Jonathan Casper for their input and work on this feature.
2 July 2013
- Assembly Data Hubs
We are pleased to announce a new feature in the UCSC Genome Browser:
Assembly Data Hubs.
Assembly Data Hubs extend the functionality of Track Data Hubs to
assemblies that are not hosted natively on the Browser. Assembly Data
Hubs were developed to address the increasing need for researchers to
annotate sequence for which UCSC does not provide an annotation
database. They allow researchers to include the underlying reference
sequence, as well as data tracks that annotate that sequence. Sequence
is stored in the UCSC twoBit format, and the annotation tracks are
stored in the same manner as Track Data Hubs.
To read more about using Assembly Data Hubs, or about creating your
own, see these guides:
Many thanks to Hiram Clawson, Brian Raney, and Pauline Fujita for their work on this feature.
2 July 2013
- New Gene Alleles feature on the details pages of UCSC genes
We are excited to announce the release the new Gene Alleles feature on
the details pages of UCSC genes. For each protein-coding gene in the
UCSC Genes track, variant data from the 2,184 (per autosome) phased
chromosomes from Phase 1 of the 1000 Genomes Project have been
distilled into "gene haplotype alleles." Each haplotype allele is a
distinct set of variants found on at least one of the 1000 Genomes
subject chromosomes. For each haplotype, we display its frequency in
the 1000 Genomes populations and indicate the frequency with which it
occurs homozygously in each population. Unexpected frequencies of
occurrence may thus be used to identify alleles that merit further
study. Predicted protein sequence for common haplotypes can also be
displayed, allowing differences among alleles to be used to identify
differences at the amino acid level.
To see the Gene Alleles feature, go to the details page for any
protein-coding gene in the UCSC Genes track and click the "Gene
Alleles" link in the "Page Index" matrix. This
will take you to the "Common Gene Haplotype Alleles" section. For
more information on this feature please see this help doc:
Many thanks to Tim Dreszer, Brooke Rhead and Pauline Fujita for their work on this feature.
28 June 2013
- New UCSC Genes Track Released for GRCh37/hg19
We're happy to announce the release of an updated UCSC Genes
track for the GRCh37/hg19 human Genome Browser.
The new release has 82,960 total transcripts, compared with
80,922 in the previous version. The total number of canonical
genes has increased from 31,227 to 31,848. Comparing the new
gene set with the previous version:
74,657 transcripts did not change between versions.
88 transcripts were not carried forward to the new version.
5,556 transcripts are "compatible" with those in the previous set,
meaning that the two transcripts show consistent splicing.
In most cases, the old and new transcripts differ in the
lengths of their UTRs.
621 transcripts overlap with those in the previous set but
do not show consistent splicing, i.e., they contain overlapping
introns with differing splice sites.
Many thanks to Brian Raney, Jim Kent, and Luvina Guruvadoo
for their work on this track!
27 June 2013
- New Official European Mirror Released
The UCSC Genome Browser is pleased to announce the
introduction of a new mirror site to serve our users
in Europe. Genome-euro is an official European mirror
site of the UCSC Genome Browser, at
http://genome-euro.ucsc.edu. The server is physically
located at the Universität Bielefeld Center for
Biotechnology in Bielefeld, Germany, and is administered
by UCSC. Genome-euro is meant to be an alternate, faster
access point for those Browser users who are geographically
closer to central Europe than to the western United States.
All functionality will be the same as on the US server,
although Custom Tracks will not be transfered. Saved Sessions
containing Custom Tracks will require some manual intervention.
When European users navigate to the US server home page
and click the "Genomes" menu item, they will receive a
notification that they have been
redirected to the more geographically-appropriate server.
They will have the option to remain on the US server, as
described in our
documentation.
The backup mirror in Aarhus, Denmark will continue to serve as an
emergency site in the event of the official sites in California
and Germany malfunctioning.
We wish to express our special thanks to our colleagues at the
Universität Bielefeld Bioinformatics, especially Jens Stoye,
for making this possible.
26 June 2013
- Suggestion Box Released
Due to popular demand, we have created a suggestion box for track, assembly,
tool, and other requests. All suggestions will be assigned a reference
number so that you may follow up on their progress with our staff. Please
limit the use of this form to requests for new features; questions and reports
of problems about existing features and data should continue to be directed to
our mailing lists. You may reach the suggestion box from the
Contact Us page or by clicking here.
12 June 2013
- Ferret Genome Browser Released
A Genome Browser is now available for the Ferret
(Mustela putorius furo) assembly released by the Ferret Genome Sequencing Consortium
April 2011 (version MusPutFur1.0, UCSC version musFur1).
Please note the assembly construction details.
For more information and statistics about this assembly,
see the NCBI assembly record for
MusPutFur1.0.
Bulk downloads of the sequence and annotation data may be obtained from the Genome
Browser FTP server
or the
Downloads
page. Please observe the
conditions for use
when accessing and using these data sets. The annotation tracks for this browser
were generated by UCSC and collaborators worldwide. See the
Credits page for a detailed
list of the organizations and individuals who contributed to this release.
22 May 2013
- Gibbon Genome Browser Released
A Genome Browser is now available for the Gibbon
(Nomascus leucogenys) assembly released by the Gibbon Genome Sequencing Consortium
October 2012 (version Nleu_3.0, UCSC version nomLeu3).
Please note the assembly construction details.
For more information and statistics about this assembly,
see the NCBI assembly record for
Nleu_3.0.
Bulk downloads of the sequence and annotation data may be obtained from the Genome
Browser FTP server
or the
Downloads
page. Please observe the
conditions for use
when accessing and using these data sets. The annotation tracks for this browser
were generated by UCSC and collaborators worldwide. See the
Credits page for a detailed
list of the organizations and individuals who contributed to this release.
09 April 2013
- The UCSC Cancer Genomics Browser Has a New Look!
The UCSC Cancer Genomics group has recently remodeled the interface of the
Cancer Genomics Browser
to make it easier to navigate and more intuitive to
display, investigate, and analyze cancer genomics data and
associated clinical information. This tool provides access to many types of
information—biological pathways, collections of genes, genomic and clinical
information—that can be used to sort, aggregate, and perform statistical
tests on a group of samples.
The Cancer Browser currently displays 473 datasets of 25 cancers from
The Cancer Genome Atlas
(TCGA) as well as data from the
Cancer Cell
Line Encyclopedia (CCLE) and Stand Up To Cancer.
We are pleased to announce the release of three tracks derived
from dbSNP build 137, available on the mouse assembly (GRCm38/mm10).
dbSNP build 137 is available at NCBI. The new tracks contain
additional annotation data not included in previous dbSNP tracks,
with corresponding coloring and filtering options in the Genome
Browser.
As was the case for previous annotations based on dbSNP data, there are three
tracks in this release.
One is a track containing all mappings of reference SNPs to the
mouse assembly, labeled "All SNPs (137)". The other two tracks
are subsets of this track and show interesting and easily defined
subsets of dbSNP:
Common SNPs (137): uniquely mapped variants that appear in
at least 1% of the population
Mult. SNPs (137): variants that have been mapped to more
than one genomic location
By default, only the Common SNPs (137) are visible; other
tracks must be made visible using the track controls.
You will find the three SNPs (137) tracks on the Mouse Dec.
2011 (GRCm38/mm10) browser in the "Variation and Repeats" group.
The tracks were produced at UCSC by Angie Hinrichs and Luvina Guruvadoo.
11 February 2013 -
Denisova tracks released on hg19 browser
In conjunction with the publication of the paper by Meyer et al.
A High-Coverage Genome Sequence from an Archaic Denisovan Individual
the UCSC Genome Browser is hosting a set of new tracks. Briefly, Meyer et al.
applied a novel single-stranded DNA library preparation method to DNA previously
extracted from 40mg of a phalanx bone excavated from Denisova Cave in the
Altai Mountains in southern Siberia.
Two supporting datasets and one analysis dataset are now available in the Genome Browser:
Modern Human Variants: variant calls made from sequence reads of eleven individuals
mapped to the human genome, used in statistical analyses to put the divergence of the
Denisova genome into perspective with regard to present-day humans.
Denisova Sequence: high-coverage (30X) sequence reads from an archaic Denisovan
individual mapped to the human genome reference assembly.
Modern Human Derived, Denisova Ancestral: mutations in the modern human lineage
that rose to fixation or near fixation since the split from the last common
ancestor with Denisovans, along with predicted functional effects from Ensembl's
Variant Effect Predictor (VEP).
We'd like to thank Richard Green and the many authors of the Science paper
for providing the UCSC Genome Browser with these data.
We'd also like to acknowledge the hard work of the UCSC Genome Browser staff
who pulled together the annotations and information for these tracks:
Angie Hinrichs and Pauline Fujita.
25 January 2013 -
Southern White Rhinoceros Genome Browser Released
A Genome Browser is now available for the Southern White Rhinoceros
(Ceratotherium simum simum) assembly released by the Broad
Institute in May 2012 (Broad version cerSimSim1.0, UCSC version cerSim1). This
genome was sequenced and assembled at the Broad Institute using samples
provided by Dr. Oliver Ryder at the San Diego Zoo Institute for Conservation
Research. For more information and statistics about this assembly,
see the NCBI assembly record for
CerSimSim1.0.
Bulk downloads of the sequence and annotation data may be obtained from the Genome
Browser FTP server
or the
Downloads
page. Please observe the
conditions for use
when accessing and using these data sets. The annotation tracks for this browser
were generated by UCSC and collaborators worldwide. See the
Credits page for a detailed
list of the organizations and individuals who contributed to this release.
22 January 2013 -
New Baboon (papAnu2) Assembly Now Available in the Genome Browser
We are pleased to announce the release of a Genome Browser for the March 2012
assembly of the Olive Baboon, Papio anubis (Baylor Panu_2.0, UCSC version
papAnu2). The whole genome shotgun assembly was provided by
The Baylor College of Medicine Human Genome Sequencing Center.
There are 72,500 scaffolds with a total size of 2,948,380,710 bases.
Bulk downloads of the sequence and annotation data are available via the Genome
Browser
FTP server
or the
Downloads
page. These data have
specific conditions for use.
The baboon (papAnu2) browser annotation tracks were generated by UCSC and
collaborators worldwide. See the
Credits page for a detailed
list of the organizations and individuals who contributed to this release.
15 January 2013 -
New Lamprey (petMar2) Assembly Now Available in the Genome Browser
We are pleased to announce the release of a Genome Browser for the September 2010
assembly of the Lamprey, Petromyzon marinus (WUGSC 7.0, UCSC version
petMar2). The whole genome shotgun assembly was provided by
The Genome Institute at Washington University.
There are 25,006 scaffolds with a total size of 885,550,958 bases.
Bulk downloads of the sequence and annotation data are available via the Genome
Browser
FTP server
or the
Downloads
page. These data have
specific conditions for use.
The lamprey (petMar2) browser annotation tracks were generated by UCSC and
collaborators worldwide. See the
Credits page for a detailed
list of the organizations and individuals who contributed to this release.
20 December 2012 -
28 New Vertebrate Assemblies!
Over the past several weeks, we have released 28 new vertebrate assemblies on the
public Genome Browser website, featuring 22 new species and 6 assembly updates.
These assemblies were added to support the 60-species Conservation track on the
latest mouse assembly (mm10/GRCm38). Several of these species were originally
sequenced and assembled for the Mammalian Genome Project (Lindblad-Toh
et al., Nature 2011)*.
Primates:
Baboon (Papio hamadryas) papHam1 –
Pham_1.0 (Nov. 2008) from the Baylor College of Medicine HGSC
Bushbaby (Otolemur garnettii) otoGar3 –
OtoGar3 (Mar. 2011) from the Broad Institute
Chimpanzee (Pan troglodytes) panTro4 –
Build 2.1.4 (Feb. 2011) from the Chimpanzee Sequencing and Analysis Consortium
Gibbon (Nomascus leucogenys) nomLeu2 –
Nleu1.1 (Jun. 2011) from the Gibbon Genome Sequencing Consortium
Mouse lemur (Microcebus murinus) micMur1 –
MicMur1.0 (Jul. 2007) from the Broad Institute
Rhesus macaque (Macaca mulatta) rheMac3 –
CR_1.0 (Oct. 2010) from the Beijing Genomics Institute
Squirrel monkey (Saimiri boliviensis) saiBol1 –
SaiBol1.0 (Oct. 2011) from the Broad Institute
Tarsier (Tarsius syrichta) tarSyr1 –
Tarsyr1.0 (Aug. 2008) from WUSTL and the Broad Institute
Other mammals:
Alpaca (Vicugna pacos) vicPac1 –
VicPac1.0 (Jul. 2008) from the Broad Institute
Armadillo (Dasypus novemcinctus) dasNov3 –
DasNov3 (Dec. 2011) from the Baylor College of Medicine HGSC
Cat (Felis catus) felCat5 –
Felis_catus-6.2 (Sep. 2011) from the International Cat Genome Sequencing Consortium
Dolphin (Tursiops truncatus) turTru2 –
Ttru_1.4 (Oct. 2011) from the Baylor College of Medicine HGSC
Hedgehog (Erinaceus europaeus) eriEur1 –
Draft_v1 (Jun. 2006) from the Broad Institute
Kangaroo rat (Dipodomys ordii) dipOrd1 –
DipOrd1.0 (Jul. 2008) from Baylor College of Medicine HGSC and the Broad Institute
Manatee (Trichechus manatus latirostris) triMan1 –
TriManLat1.0 (Oct. 2011) from the Broad Institute
Megabat (Pteropus vampyrus) pteVam1 –
PteVap1.0 (Jul. 2008) from the Broad Institute
Naked mole rat (Heterocephalus glaber) hetGla2 –
HetGla_female_1.0 (Jan. 2012) from the Broad Institute
Pig (Sus scrofa) susScr3 –
Sscrofa10.2 (Aug. 2011) from the Swine Genome Sequencing Consortium
Pika (Ochotona princeps) ochPri2 –
OchPri2 (Jul. 2008) from the Broad Institute
Rock hyrax (Procavia capensis) proCap1 –
Procap1.0 (Jul. 2008) from the Baylor College of Medicine HGSC
Shrew (Sorex araneus) sorAra1 –
SorAra1.0 (Jun. 2006) from the Broad Institute
Sloth (Choloepus hoffmanni) choHof1 –
ChoHof1.0 (Jul. 2008) from the Broad Institute
Squirrel (Spermophilus tridecemlineatus) speTri2 –
SpeTri2.0 (Nov. 2011) from the Broad Institute
Tree shrew (Tupaia belangeri) tupBel1 –
Tupbel1.0 (Dec. 2006) from the Broad Institute
Budgerigar (Melopsittacus undulatus) melUnd1 –
v6.3 (Sep. 2011) from WUSTL
Coelacanth (Latimeria chalumnae) latCha1 –
LatCha1 (Aug. 2011) from the Broad Institute
Nile tilapia (Oreochromis niloticus) oreNil2 –
OreNil1.1 (Jan. 2011) from the Broad Institute
Our sincere thanks to the many organizations who contributed to the release
of these datasets. We'd also like to acknowledge the Genome Browser
staff who worked on this release: Hiram Clawson, Chin Li, Brian Raney,
Brooke Rhead, Steve Heitner, Pauline Fujita, Luvina Guruvadoo, Greg Roe, and
Donna Karolchik. Please see the Genome Browser
credits page for complete acknowledgment
information and data use restrictions. All datasets may be downloaded from our
ftp server or
downloads page.
We regret that we don't have the resources to support the many other
genomics research communities who would like us to visualize their data
in our browser. However, we can provide you with information for setting up
your own browser or track hub to display your data, as well as links to
other visualization resources on the web that are specific to your
genome of interest. Feel free to contact our
mail list for more information.
14 December 2012
- Reduced Coverage During the Holidays
The UCSC campus will be closed for the holidays from December 22, 2012 through
January 1, 2013. The Genome Browser will still be available;
however, our backup systems will be offline for two days, December 27 and 28.
During this time if we experience any issues, associated fixes are likely to be
delayed. The help desk will also be minimally staffed during this period. We
will be monitoring the mailing lists for urgent messages, but the bulk of the
questions will go unanswered until early January.
07 December 2012
- dbSNP 137 Available for hg19
We are pleased to announce the release of four tracks derived
from dbSNP build 137, available on the human assembly (GRCh37/hg19).
dbSNP build 137 is available at NCBI. The new tracks contain
additional annotation data not included in previous dbSNP tracks,
with corresponding coloring and filtering options in the Genome
Browser.
As was the case for previous annotations based on dbSNP data, there are four tracks
in this release.
One is a track containing all mappings of reference SNPs to the
human assembly, labeled "All SNPs (137)". The other three tracks
are subsets of this track and show interesting and easily defined
subsets of dbSNP:
Common SNPs (137): uniquely mapped variants that appear in
at least 1% of the population
Flagged SNPs (137): uniquely mapped variants, excluding
Common SNPs, that have been flagged by dbSNP as "clinically
associated"
Mult. SNPs (137): variants that have been mapped to more
than one genomic location
By default, only the Common SNPs (137) are visible; other
tracks must be made visible using the track controls.
You will find the four SNPs (137) tracks on the Human Feb.
2009 (GRCh37/hg19) browser in the "Variation and Repeats" group.
The tracks were produced at UCSC by Angie Hinrichs and Steve Heitner.
27 November 2012 -
New UCSC Genes Track Released for Mouse
We're happy to announce the release of a new UCSC Genes
track for the GRCm38/mm10 mouse Genome Browser.
The new release has 59,121 transcripts, compared with
55,419 in the previous version on mm9. The total number
of canonical genes has increased from 28,661 to 31,227.
Comparing the new gene set with the previous version:
48,739 transcripts did not change between versions.
423 transcripts were not carried forward to the new version.
5,108 transcripts are "compatible" with those in the previous
set, meaning that the two transcripts show consistent splicing.
1,037 transcripts overlap with those in the previous set.
More details about the new UCSC Genes track can be found on
the UCSC Genes track description page. Also, please note that
GRCm38/mm10 is now the default mouse assembly on the Genome Browser Gateway.
Many thanks to Brian Raney, Jim Kent, and Luvina Guruvadoo
for their work on this track!
14 November 2012 -
ENCODE Tutorials Available from OpenHelix
OpenHelix and the UCSC Bioinformatics group have collaborated
to provide free access to the newly
updated ENCODE tutorial until the end of February 2013.
The online tutorial suite, which runs on most Internet browsers,
teaches users how to access
the ENCODE data in the UCSC Genome Browser. The
approximately 60-minute tutorial was created by OpenHelix
in conjunction with the
UCSC Bioinformatics Group, and can be viewed at no cost at
http://www.openhelix.com/ENCODE2. The
material has been updated to reflect recent changes
to the UCSC Genome Browser, and can be viewed sequentially or navigated
using chapters and forward/backward sliders.
The original, older tutorial is still available at
http://www.openhelix.com/ENCODE.
In addition to the tutorial, users can access other useful
training materials including the animated PowerPoint slides
used as a basis for the tutorial, a suggested script for the
slides, slide handouts, and exercises.
17 September 2012 -
Retiring the Proteome Browser
We are announcing the imminent retirement of the Proteome Browser.
The Proteome Browser was introduced in 2003 to provide access to
protein-specific information independent of the genomic details
presented in the Genome Browser. Since then we've incorporated much
of this information into the UCSC Genes details page accessible from the
Genome Browser, and into the columns of the Gene Sorter. Our decision to
retire this tool was based on its low usage and our desire to focus our
work on the more frequently used UCSC Genes track and the Gene Sorter.
Access to the databases that supported the Proteome Browser (uniProt and proteome)
will still be available through the Table Browser and our public MySQL
server.
16 August 2012 - Announcing a Genome Browser for
the Medium ground finch
We have released a browser for the Medium ground finch,
Geospiza fortis, renowned as one of naturalist Charles
Darwin's Galapagos finches. This species, which has been the
subject of many evolutionary studies, is one of a group of
birds that evolved over a few million years from a single
ancestral species into multiple species whose beak sizes and
shapes are specialized for using different food resources. The
phenotypic diversity of these birds contributed to Darwin's
theory of evolution. The significance of this genome assembly is
described in the August 16, 2012,
press release issued by the UCSC Center for
Biomolecular Science and Engineering (CBSE).
The initial Medium ground finch genome assembly (GeoFor_1.0,
UCSC version geoFor1) is the product of a collaboration between
the Genome 10K project and Beijing Genomics Institute (BGI) to
sequence 100 vertebrate species, and is the first to be
released in the UCSC Genome Browser. For more information about
the G. fortis genome, see the
NCBI website.
Bulk downloads of the sequence and annotation data are available
via the Genome Browser
FTP server or the
Downloads page.
The browser annotation tracks were generated by UCSC and
collaborators worldwide. See the
Credits
page for a detailed list of the organizations and individuals
who contributed to this release. We'd like to thank BGI for
contributing the data for this assembly and acknowledge the
UCSC staff members who released this browser: Hiram Clawson and
Greg Roe.
14 August 2012 - Changes to our website
We are pleased to announce a few changes to the look and feel of the Genome
Browser website. In addition to a new font throughout the site, the first thing you
might notice is
a new menu bar across the top of many of the pages. We have reorganized the
navigation on our web
applications with you in mind; we hope you find it more intuitive!
Additionally, we greatly simplified the search mechanism by
collapsing all search methods into a single box.
In this box, you can search for chromosomal coordinate ranges, gene names,
accession numbers,
keywords, etc. For a complete list of ways to query the browser data, see
Querying the Genome
Browser.
16 July 2012 - Tasmanian Devil
Assembly Now Available in Genome Browser
We are pleased to announce the release of a Genome Browser
for the February 2011 Tasmanian devil assembly,
Sarcophilus harrisii (WTSI version Devil_refv7.0,
UCSC version sarHar1). The Tasmanian devil, which is
native to the island of Tasmania, is at risk of extinction due
to a transmissible facial cancer. The devil population
in Tasmania has declined by more than 80% since the first
time the disease was observed 14 years ago.
This draft assembly, created by the
Wellcome Trust Sanger Institute,
was sequenced using Illumina reads. This completed genome
is the first step towards finding genetic mutations in the
transmissible cancer, which will help
researchers understand the disease and its spread.
Bulk downloads of the sequence and annotation data are available
via the Genome Browser
FTP server or the
Downloads
page. The Tasmanian devil browser
annotation tracks were generated by UCSC and collaborators worldwide.
See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
06 July 2012 - Retirement of hgText CGI
We are announcing the imminent retirement of the hgText
CGI. hgText was the original version of the Table Browser,
and was replaced by the new CGI, hgTables, in 2004. A very
small number of our users still access the database
using the old hgText CGI. We plan to remove hgText
from our site on July 24, 2012, after which all users must
use hgTables.
19 June 2012 - Many New
Assemblies Available in the Browser!
With the abundance of new vertebrate assemblies available in
GenBank, the UCSC Genome Browser team has streamlined its
browser release pipeline in the effort to keep pace. In the past
week we have released a new browser on the Western painted
turtle and updated assemblies for the cow, rat, and chicken.
Browsers for the lesser hedgehog tenrec and the latest dog
assembly should be available later this week, for a total of 18
assemblies released in the past half year. You can
expect many new assemblies to show up on our website in upcoming
months, along with broader multiple alignment annotations on
selected organisms that include many of the new assemblies.
Keep in mind that some of these new assemblies may not yet be
fully populated with annotation tracks. Some data, such as the
data underlying genes and SNPs tracks, may not be immediately
available, and other annotations (e.g., comparative genomics
tracks) may take a while to generate. As always, our mandated
focus is on vertebrates, with a particular emphasis on richly
annotating the human genome, although we do provide occasional
updated assemblies for other selected model organisms (fly,
worm, yeast).
We regret that we don't have the resources to support the many
other genomics research communities who would like us to
visualize their data in our browser, but we can provide you
with information for setting up your own browser or track hub
to display your data, as well as links to other visualization
resources on the web that are specific to your genome of
interest. Feel free to contact us
for more information.
Newly released assemblies:
Cow (Bos taurus) bosTau7 –
Btau_4.6.1 (Oct. 2011) from the Bovine Genome Sequencing
Consortium and Baylor College of Medicine
Rat (Rattus norvegicus) rn5 –
RGSC Rnor_5.0 (Oct. 2011) from the Rat Genome Sequencing
Consortium
Chicken (Gallus gallus) galGal4
– Gallus_gallus-4.0 (Nov. 2011) from the International
Chicken Genome Consortium
Western painted turtle (Chrysemys picta bellii)
chrPic1 – Chrysemys_picta_bellii-3.0.1 (Dec. 2011)
from the International Painted Turtle Genome Sequencing Consortium
Lesser hedgehog tenrec (Echinops telfairi)
echTel1 – echTel1 (Jul. 2005) from the Broad
Institute (pending)
Dog (Canis familiaris) canFam3
– v3.1 (Sep. 2011) from the Broad Institute (pending)
Released in the past half year:
Mouse (Mus musculus) mm10 –
GRCm38 (Dec. 2011) from the Mouse Genome Reference Consortium
Cow (Bos taurus) bosTau6 –
Bos_taurus_UMD_3.1 (Nov. 2009) from the University of Maryland
Fugu (Takifugu rubripes) fr3 –
FUGU5 (Oct. 2011) from the International Fugu Genome Sequencing
Consortium
Gibbon (Nomascus leucogenys) nomLeu1
– Nleu1.0 (Jan. 2010) from the Gibbon Genome Sequencing
Consortium
Gorilla (Gorilla gorilla gorilla) gorGor3
– gorGor3.1 (May 2011) from the Wellcome Trust Sanger
Institute
Microbat (Myotis lucifugus) myoLuc2
– Myoluc2.0 (Jul. 2010) from the Broad Institute
Naked mole-rat (Heterocephalus glaber)
hetGla1 – HetGla_1.0 (Jul. 2011) from the Beijing
Genomics Institute
Tammar wallaby (Macropus eugenii) macEug2
– Meug_1.1 (Sep. 2009) from the Tammar Wallaby Genome
Sequencing Consortium
Turkey (Meleagris gallopavo) melGal1
– Turkey_2.01 (Dec. 2009) from the Turkey Genome Consortium
Western clawed frog (X. tropicalis)
xenTro3 – v4.2 (Nov. 2009) from the DOE Joint
Genome Institute
C. elegansce10 – WS220
(Oct. 2010) from WormBase
S. cerevisiaesacCer3 –
SacCer_Apr2011 (Apr. 2011) from the Saccharomyces Genome Database
Bulk downloads of the sequence and annotation data for these
assemblies are available via the Genome Browser
FTP server or the
Downloads page. Be sure to check the
credits page for data use
restrictions and acknowledgments.
Many thanks to the sequencing and assembly groups, as well as
NCBI's GenBank, for making these genomes available for public
use. We'd also like to acknowledge Hiram Clawson, Chin Li, and
our hard-working QA team for putting together these browsers.
15 May 2012 - New Fugu
(fr3) Assembly Now Available in the Genome Browser
Bulk downloads of the sequence and annotation data are available via the Genome
Browser
FTP server or the
Downloads page.
These data have
specific conditions for use. The fugu (fr3)
browser annotation tracks were generated by UCSC and
collaborators worldwide. See the Credits
page for a detailed list of the organizations and individuals who contributed
to this release.
15 May 2012 - Naked Mole-Rat
Assembly Now Available in Genome Browser
We are pleased to announce the release of a Genome Browser
for the July 2011 Naked mole-rat, Heterocephalus glaber
(BGI version HetGla1.0, UCSC version hetGla1). This draft assembly,
produced by the
Beijing Genomics Institute, has been sequenced using
Illumina reads with a sequencing depth of >20x. There are
39,266 scaffolds with a total size of 2,643,961,837 bases.
The N50 size of the scaffolds is 1,603,177 bases with 502
scaffolds larger, and 38,764 scaffolds smaller. The mitochondrial
sequence is also available as the virtual chromosome "chrM".
Bulk downloads of the sequence and annotation data are available
via the Genome Browser
FTP server or the
Downloads page. These data have
specific conditions
for use. The Naked mole-rat browser annotation tracks were
generated by UCSC and collaborators worldwide. See the
Credits page
for a detailed list of the organizations and individuals who
contributed to this release.
8 May 2012 - OpenHelix
to Conduct Free Genome Browser Webinars in May
OpenHelix
is conducting two free webinars on the UCSC Genome Browser:
UCSC Genome Browser: An Introduction
(Thursday, May 17, 1pm EDT) -- designed for new users
of the UCSC Genome Browser and those who want to improve their
skills at basic navigation and display.
UCSC Table Browser and Custom Tracks
(Thursday, May 24, at 1pm EDT) -- advanced Genome Browser
topics, including creating Custom Tracks and using the Table
Browser.
The webinars will last approximately 1hr 15min.
Seating is limited and registration is required. Slides may be
downloaded from the OpenHelix website prior to the webinar.
OpenHelix provides training materials and programs on hundreds
of free, publicly accessible bioinformatics and genomics
resources. To browse their entire collection of UCSC genomics
tutorials, go to the OpenHelix
UCSC training page.
2 May 2012 - OpenHelix
Releases Updated Genome Browser Tutorials
OpenHelix
has released updated versions of two Genome Browser tutorial
suites:
Each suite contains an online, narrated tutorial that highlights
and explains the features and functionality needed to use the
UCSC tools effectively, and a collection of training materials
that includes the PowerPoint slides used as a basis for the
tutorial, a suggested script for the slides, slide handouts, and
exercises. These materials, all of which are free, can be used
as a reference for users or as a ready-made presentation for
training others on the use of the Genome Browser.
For more information on the tutorials and OpenHelix, see the
OpenHelix
press release.
18 April 2012 - GRC Planning
Phase for GRCh38 Human Reference Assembly
The Genome Reference Consortium (GRC) plans to
update the human reference assembly to GRCh38 in the summer of
2013. This revision is aimed at addressing issues found with the
current model for representing genome assemblies, which uses a
single, preferred tiling path to produce a single consensus
representation of the genome. Subsequent analysis has
shown that for most mammalian genomes a single tiling path is
insufficient to represent a genome in regions with complex
allelic diversity. The GRC is working to create assemblies that
better represent this diversity and provide more robust
substrates for genome analysis.
If you have questions, concerns or feedback about the plans for
the GRCh38 assembly, the GRC would
like your input.
07 March 2012 - New Mouse
Browser Available
We have released the latest Genome Browser for the December 2011
Mouse genome assembly produced by the
Mouse Genome Reference Consortium (Genome Reference Consortium
GRCm38, UCSC version mm10).
This version, which includes approximately 2.6 Gb of sequence,
is considered to be "essentially complete". The assembly includes
chromosomes 1-19, X, Y, M (mitochondrial DNA) and chr*_random
(unlocalized) and chrUn_* (unplaced clone contigs).
Note that the UCSC mm10 database contains only the
reference strain C57BL/6J.
Bulk downloads of the sequence and annotation data are available
via the Genome Browser FTP
server or the
Downloads
page. The Mouse browser annotation tracks were generated by UCSC
and collaborators worldwide. See the Credits page for a detailed list of the
organizations and individuals who contributed to this release.
29 February 2012 - RGD Genes Available for rn4
We are pleased to announce the release of RGD Genes for rat
(Baylor 3.4/rn4). This track shows protein-coding gene annotations
curated by RGD. This track
replaces UCSC Known Genes as the main gene track for this assembly.
We'd like to thank RGD for providing the base annotations for this
track. The RGD Genes track was produced by Fan Hsu, Mary Goldman and
Hiram Clawson.
10 February 2012 -
dbSNP 135 Available for hg19
We are pleased to announce the release of four tracks derived
from dbSNP build 135, available on the human assembly (GRCh37/hg19).
dbSNP build 135 is available at NCBI. The new tracks contain
additional annotation data not included in previous dbSNP tracks,
with corresponding coloring and filtering options in the Genome
Browser.
As was the case with dbSNP build 132, there are four tracks in this release.
One track, labeled "All SNPs (135)", contains all mappings of reference SNPs to the
human assembly. The other three tracks
are subsets of this track and show interesting and easily defined
subsets of dbSNP:
Common SNPs (135): uniquely mapped variants that appear in
at least 1% of the population
Flagged SNPs (135): uniquely mapped variants, excluding
Common SNPs, that have been flagged by dbSNP as "clinically
associated"
Mult. SNPs (135): variants that have been mapped to more
than one genomic location
By default, only the Common SNPs (135) are visible; other
tracks must be made visible using the track controls.
You will find the four SNPs (135) tracks on the Human Feb.
2009 (GRCh37/hg19) browser in the "Variation and Repeats" group.
Many thanks to dbSNP at NCBI for the data, and to
Mary-Claire King at the University of Washington for helpful
comments that motivated us to enhance our dbSNP annotations. The
tracks were produced at UCSC by Angie Hinrichs and Brooke Rhead.
02 February 2012 - New UCSC
Genes Track Released for GRCh37/hg19
We're happy to announce the release of an updated UCSC Genes
track for the GRCh37/hg19 human Genome Browser. This release
includes more noncoding transcripts based on data from
Rfam
and from the
tRNA Genes
track contributed by the Todd Lowe lab at UCSC.
The new release has 80,922 total transcripts, compared with
77,614 in the previous version. The total number of
canonical genes has increased from 27,297 to 31,227.
Comparing the new gene set with the previous version:
24,804 transcripts did not change between versions.
483 transcripts were not carried forward to the new
version.
46,367 transcripts are "compatible" with those in the
previous set, meaning that the two transcripts show
consistent splicing. In most cases, the old and new
transcripts differ in the lengths of their UTRs.
5,960 transcripts overlap with those in the previous
set but do not show consistent splicing, i.e., they contain
overlapping introns with differing splice sites.
Additionally, several improvements where made to the UCSC
Genes build pipeline:
We developed new genomic alignment protocols for
aligning short sequences, facilitating the expansion of the
noncoding RNA content.
We changed the way that gene symbols are assigned to
transcripts so that names from curated sources are favored
over names coming directly from GenBank mRNA records. This
change resolved several confusing naming issues reported to
us by users.
We tracked down and corrected a bug in the pipeline that
was causing a number of poor quality protein mappings to
displace high quality protein mappings.
We have started producing two new tables,
knownGeneTxMrna and knownGeneTxPep, that contain sequence
derived from the genome rather than from the mRNA used for
the transcript.
Many thanks to Melissa Cline, Jim Kent, Brian Raney, Mark
Diekhans, and Brooke Rhead for their work on this track!
23 January 2012 - Wallaby
Browser Available
We have released a Genome Browser for the September 2009
genome assembly of the Tammar Wallaby, Macropus eugenii
(TWGS version Meug_1.1, UCSC version macEug2).
This assembly, which has been sequenced to 2X coverage, was
produced by the Tammar Wallaby Genome Sequencing Consortium,
a collaboration between the Baylor College of Medicine
Human Genome Sequencing Center and the
Australian Genome Research Facility.
We'd like to thank the Tammar Wallaby Genome Sequencing
Consortium for providing this assembly. The wallaby Genome
Browser and annotation tracks were produced by Chin Li and
Luvina Guruvadoo. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
3 January 2012 - Roadmap
Epigenomics Now Available through Data Hub at Washington
University
We are pleased to announce the release of the Roadmap
Epigenomics data on the UCSC Genome Browser through our
Data Hub function. The Roadmap Epigenomics Project is part
of The NIH Common Fund's
Epigenomics Program.
It was launched with the goal of producing a public resource
of human epigenomic data to catalyze basic biology
and disease-oriented research. The Consortium leverages
experimental pipelines built around next-generation
sequencing
technologies to map DNA methylation, histone modifications,
chromatin accessibility and small RNA transcripts in stem
cells and primary ex vivo tissues selected to represent the
normal counterparts of tissues and organ systems frequently
involved in human disease. The Consortium expects to deliver
a collection of normal epigenomes that will provide a
framework or reference for comparison and integration within
a broad array of future studies.
All data were produced and processed by the
Roadmap Epigenomics Mapping Consortium,
and will be periodically updated. Genome Browser tracks were
constructed and hosted by VizHub at Washington University in St.
Louis. Tracks are available at UCSC Genome Browser via the
Data Hub function, or follow this
link.
The Roadmap Epigenomics Mapping Consortium is responsible
for the quality of the data.
19 December 2011 - VariantCall Format (VCF) Now Supported in Genome Browser
We are pleased to announce that the UCSC Genome Browser
now supports Variant Call Format (VCF). VCF is a flexible
and extendable line-oriented text format developed by the
1000 Genomes Project for releases of single nucleotide
variants, indels, copy number variants and structural
variants discovered by the project. Similar to bigBed,
bigWig and BAM, the Browser transfers only the portions of
VCF files necessary to display
viewed regions, making VCF a fast and attractive option for
large data sets. VCF files will need to be compressed and
indexed using the tabix package available from
SAMtools. This new format is available
for use in custom tracks and data hubs. For more information
about VCF and tabix, please see our
VCF Track Format help page.
7 November 2011 - UMD Cow Assembly Now Available in Genome Browser
In response to the many requests from the bovine research
community, we now offer the University of Maryland (UMD)
Bos taurus assembly in the Genome Browser, in
addition to the assemblies produced by the Baylor College
of Medicine Human Genome Sequencing Center. The UMD v3.1
assembly (Nov. 2009, UCSC bosTau6) was produced by the
UMD Center for Bioinformatics and
Computational Biology (CBCB) in College Park, MD.
The UMD 3.1 assembly is based on reads downloaded from
the NCBI Trace Archive, most of which were sequenced by
the Baylor College of Medicine. UMD reports that they were
able to apply several assembly improvement techniques
to produce an assembly that is substantially more accurate
and complete than previous alternative versions, as
evaluated using independent metrics. Based on UMD
statistics, this assembly provides more genome coverage,
closes thousands of gaps, corrects many erroneous
inversions, deletions, and translocations, and fixes
thousands of single-nucleotide errors. For more information,
see Zimin AV et al,
A whole-genome assembly of the domestic
cow, Bos taurus, Genome Biol. 2009;10(4).
Downloads of the UMD bovine data and annotations may be
obtained from the UCSC Genome Browser
FTP server
or Downloads page.
We'd like to thank the UMD CBCB for providing this genome
assembly. The UMD Cow Genome Browser and annotation tracks
were produced by Hiram Clawson, Chin Li, Brooke Rhead, Greg
Roe, Steve Heitner, and Donna Karolchik. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
10 October 2011 - Updated Yeast Browser Released
We are happy to announce the release of an updated browser
for the Saccharomyces cerevisiae yeast genome. The
April 2011 sacCer3 assembly corresponds to the S288c
assembly produced by the Saccharomyces Genome Database (SGD)
project. For more information on this genome, see the
SGD Genome Overview.
Downloads of the yeast data and annotations may be obtained
from the UCSC Genome Browser
FTP server or
Downloads page.
We'd like to thank the SGD for providing this genome
assembly. The S. cerevisiae Genome Browser and
annotation tracks were produced by Hiram Clawson, Greg Roe,
and Steve Heitner. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
8 September 2011
- New Navigation and Display Features
We've added several new features to the Genome Browser
that make it easier to quickly configure and navigate
around in the browser's annotation tracks window.
Automatic image resizing: The first time the annotation
track window is displayed, or after the Genome Browser has
been reset, the size of the track window is now set by
default to the width that best fits your Internet browser
window. If you subsequently resize your browser window,
you can automatically adjust the annotation track image
size to the new width by clicking the resize button
under the track image. The default width can still be
manually overridden on the Track Configuration page.
Scrolling left or right in the track window: You can now
scroll (pan) horizontally through the tracks image by clicking
on the image, dragging the cursor to the left or right,
then releasing the mouse button. The view may be scrolled
by up to one image width.
Improved drag-zoom navigation: The browser's
"drag-and-zoom" feature lets you quickly zoom to a
specific region of interest on the annotation tracks image.
To define the region you wish to zoom to, click-and-hold
the mouse button on one edge of the desired zoom area
(which can be anywhere in the tracks window), depress the
shift key, drag the mouse right or left to highlight the
selection area, then release the mouse button.
The annotation tracks image will automatically zoom to
the new region. The Genome Browser still supports the
earlier implementation of this feature, which restricted
the click-drag to the Base Position track area of the image,
but did not require the shift key to be pressed.
Reordering groups of tracks:
You can now vertically reposition an entire group of
associated tracks in the tracks image (such as all the
displayed subtracks in a composite track) by clicking and
holding the gray bar to the left of the tracks,
dragging the group to the new position, then releasing
the mouse button. To move a single track up or down, click
and hold the mouse button on the side label, drag the
highlighted track to the new position, then release the
mouse button.
If you haven't yet tried the browser's right-click
menu for quick access to frequently used track
configuration features and functionality, read more
here.
18 August 2011
- New Feature: Track Data Hubs
We are pleased to announce a new feature in the UCSC Genome Browser:
Track Data Hubs. Track hubs are web-accessible directories of genomic data
that can be viewed on the UCSC Genome Browser alongside native annotation
tracks. The Track Hub utility allows efficient access to data sets from around
the world through the familiar Genome Browser interface. Browser users
can display tracks from any public track hub that has been registered
with UCSC. Additionally, users can import data from unlisted hubs or can
set up, display, and share their own track hubs.
The data underlying the tracks in a hub reside on the remote server of
the data provider rather than at UCSC. The data are stored in compressed
binary indexed files in bigBed, bigWig or BAM format that contain the
data at several resolutions. When a hub track is displayed in the Genome
Browser, only the relevant data needed to support the view of the
current genomic region are transmitted rather than the entire file. The
transmitted data are cached on the UCSC server to expedite future
access. This on-demand transfer mechanism eliminates the need to
transmit large data sets across the Internet, thereby minimizing upload
time into the browser.
To check out some track data hubs that are already available, most
notably those from the NIH Roadmap Epigenomics Mapping Consortium, press
the "track hubs" button in the genome browser, or follow this link:
http://genome.ucsc.edu/cgi-bin/hgHubConnect.
To read about using hubs, or creating your own, see:
We announce today the release of our newly re-engineered OMIM
(Online Mendelian Inheritance in Man) tracks for both hg18 and
hg19. With the kind assistance of Ada Hamosh (director),
Joanna Amberger and Francois Schiettecatte of the OMIM project,
we have divided the OMIM records into three separate tracks:
OMIM Allelic Variant SNPs
Variants in the OMIM database that have associated dbSNP identifiers.
OMIM Genes
The genomic positions of gene entries in the OMIM database.
The coloring indicates the associated OMIM phenotype class.
OMIM Phenotypes - Gene Unknown
Regions known to be associated with a phenotype, but for which no
specific gene is known to be causative. This track also includes
known multi-gene syndromes.
The new tracks can be found in the Phenotype and Disease Associations
track group below the browser graphic
and are searchable by OMIM number. In most cases,
simply typing the 6-digit MIM number into the position/search box
on the Browser will take you to the record.
The OMIM data are the property of Johns Hopkins University and
will not be available for download from UCSC. Please contact the
OMIM project at omim.org for download information.
UCSC thanks engineers Fan Hsu, Brooke Rhead and Robert Kuhn for
this release.
9 June 2011 - UCSC Preview Browser Available
Early access to ENCODE and other UCSC browser data tracks under
construction is now available from the new UCSC Preview Browser site:
http://genome-preview.ucsc.edu
This site is a weekly mirror of our internal development server for
public access. Data and tools there are under construction, have not
been quality reviewed, and are subject to change at any time. We provide
this site for early access, with the warning that it is less available
and stable than our public site. For high-quality reviewed annotations
on our production server, visit our public website:
http://genome.ucsc.edu.
7 June 2011 - Updated Lizard Browser Available
We have released a Genome Browser for the May 2010
genome assembly of the green anole lizard, Anolis
carolinensis (Broad
version AnoCar2.0, UCSC version anoCar2). This assembly,
which has been sequenced to 7.1X coverage, was produced by
the Broad Institute, Cambridge, MA.
We'd like to thank the Broad Institute for providing this
assembly. The lizard Genome Browser and annotation
tracks were produced by Hiram Clawson, Brian Raney, and
Luvina Guruvadoo. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
26 May 2011 - New Release of UCSC Genes for Mouse
We've released an updated set of UCSC Genes for the mm9
(NCBI Build 37) mouse Genome Browser. This version of the
gene set was generated using the same computational
pipeline as the previous mm9 UCSC Genes, but is based on
more recent GenBank data.
The new release has 55,419 total transcripts, compared with
49,409 in the previous version. The total number of canonical
genes has increased from 27,389 to 28,661.
Comparing the new gene set with the previous version:
33,977 transcripts did not change between versions
69 transcripts were not carried forward to the new version
13,701 transcripts are "compatible" with those
in the previous set
1,662 transcripts overlap with those in the previous set
13 May 2011
- Free Browser Training
Webinar from OpenHelix
The UCSC Bioinformatics Group announces two free webinars
on the UCSC Genome Browser. The
webinars will be conducted by OpenHelix, a provider of
training on many free, publicly accessible bioinformatics
and genomics resources.
The webinars (one hour and 15 minutes long) will cover the
topics needed to effectively use the Genome Browser. The
first webinar, to be held Tuesday, May 24, 11:00-12:15 PM PDT,
Introduction to the UCSC Genome Browser, is designed
for new users of the UCSC Genome Browser, and those who want
to improve their skills at basic navigation and display.
The second webinar, UCSC Genome Browser: Custom Tracks
and Table Browser, will be held Thursday, May 26, 1:00-2:15 PM PDT.
1 May 2011 - ENCODE User's Guide and
Usability Survey
The ENCODE project has just published an overview of their ongoing large-scale
efforts to interpret the human genome sequence in the journal PLoS Biology.
A Users Guide to the Encyclopedia of DNA Elements,
highlights the scope of data production, and provides guidance for locating
and using the data. With the vast amount of data now available, the ENCODE Data Coordination Center
at UCSC continues to focus on improving the accessiblity and usability of this valuable resource.
We invite all current and prospective users of ENCODE data to participate in the
2011 ENCODE Usability Survey.
Your input will help us to make this data more accessible to the scientific community. Thank you!
18 April 2011 - dbSNP 132 Available for hg19
We are pleased to announce the release of four tracks derived from
dbSNP
build 132, available on the human assembly (GRCh37/hg19).
dbSNP build 132 is available at NCBI. The new tracks contain
additional annotation data not included in previous dbSNP tracks,
with corresponding coloring and filtering options in the Genome
Browser.
As was the case for previous annotations based on dbSNP data,
there is a track that contains all
mappings of reference SNPs to the human assembly; it is now labeled
"All SNPs (132)". Three new tracks have been added to show
interesting and easily defined subsets of dbSNP:
Common SNPs (132): uniquely mapped variants that appear in at
least 1% of the population
Flagged SNPs (132): uniquely mapped variants, excluding Common
SNPs, that have been flagged by dbSNP as "clinically associated"
Mult. SNPs (132): variants that have been mapped to more than one
genomic location
By default, only the Common SNPs (132) are visible; other tracks must
be made visible using the track controls.
The counts of distinct reference SNPs and their mappings to hg19
differ greatly among the tracks:
Track
Reference SNPs
Mappings to hg19
Common SNPs (132)
13,842,381
14,024,295 *
Flagged SNPs (132)
17,899
18,084 *
Mult. SNPs (132)
1,114,599
3,568,988
All SNPs (132)
30,030,754
33,026,121
* The Common and Flagged tracks have more mappings than SNPs due to the
alternate haplotype sequences and the pseudoautosomal regions on X and Y.
SNPs are considered uniquely mapped if they map only once to a haploid
reference genome. These regions add non-haploid sequence to the reference
genome; therefore, multiple mappings involving these regions are still
considered unique.
You will find the four SNPs (132) tracks on the Human Feb. 2009
(GRCh37/hg19) browser in the "Variation and Repeats" group.
Many thanks to dbSNP at NCBI for the data, and to
Mary-Claire King
at the University of Washington for helpful comments that motivated
us to enhance our dbSNP annotations. The tracks were produced at UCSC
by Angie Hinrichs, Brooke Rhead, Bob Kuhn, and Jim Kent.
There are 27 chromosomes: chr1 - chr26, chrX, plus the mitochondrial sequence chrM from
genbank accession NC_001941, for a total sequence length of 2,860,512,983 bases. There are
1,659,241,706 'N' bases in gaps, leaving 1,201,271,277 ACGT bases.
The genome has been sequenced using 454 FLX sequencing to 3X coverage (DNA derived from
six female sheep each sequenced with 0.5X coverage). Contigs were assembled based on alignment to
the bovine genome and ordered into ovine chromosomes using BAC-end sequences and the virtual sheep
genome.
We'd like to thank the International Sheep Genomics Consortium (ISGC)
sequencing center and Justus-Liebig-University for providing this assembly.
We'd also like to acknowledge the UCSC team who worked on
this release: Chin Li, Greg Roe, and Luvina Guruvadoo.
The sheep browser annotation tracks were generated by
UCSC and collaborators worldwide.
04 March 2011 - The Meaning of Red: Consensus on color scheme for CNVs
Consensus was reached on color standards to represent CNV loss (red)
and gain (blue) in genomics databases by DGV, NCBI, DECIPHER, UCSC and ISCA
during the 1st annual ISCA Scientific Conference.
At the recent ISCA Scientific Conference in Atlanta, GA, Nigel Carter,
representing DECIPHER, made a plea for a standardized color scheme for
representation of CNV loss (deletion) or gain (duplication). Discussions
in person and by email with leaders of major CNV/genomic databases (including
DGV, dbVar, ISCA, and the UCSC Genome Browser) resulted in the recommendation
to utilize red to represent loss/deletion (consistent with the original
convention for CGH on metaphase chromosomes) and blue to represent
gain/duplication (avoiding green which is difficult for color-blind
individuals to discriminate from red).
Announcememnt reprinted from the website for the International Standards for
Cytogenomic Arrays (ISCA)
Consortium. The UCSC Genome Browser is now conforming to this standard for the
DECIPHER track and the DGV track on human assemblies (which was released today) and
on any future tracks derived from dbVar.
Thanks to Nigel Carter, Steve Scherer, Deanna Church, Angie Hinrichs, Fan Hsu,
Pauline Fujita and Robert Kuhn.
01 March 2011 - Updated Chimpanzee Browser Released
We are happy to announce the release of a Genome Browser for
the latest release of the chimpanzee (Pan
troglodytes) genome. The Oct. 2010 assembly -- CGSC
v2.1.3, UCSC version panTro3 -- was produced by the
Chimpanzee Sequencing and Analysis
Consortium.
This assembly covers about 97 percent of the genome and is
based on 6X sequence coverage. It comprises 192,898 contigs
with an N50 length of 44 kb and 33,990 supercontigs with an
N50 length of 8.4 Mb.
Improvements introduced with the 2.1.3 assembly include the
addition of over 300,000 finishing reads and the merging in
of 640 finished BACS. Approximately 49,000 additional merges
were made in this assembly as compared with the 2.1
assembly.
The whole genome shotgun data were derived primarily from
the donor Clint, a captive-born male chimpanzee from the
Yerkes Primate Research Center in Atlanta, GA, USA.
The sequence data were assembled and organized by the
Washington University Genome Center. The underlying whole
genome shotgun data were generated at the Washington
University School of Medicine and the Broad Institute.
For detailed information about the assembly
process, see the sequencing and analysis discussion in the
GenBank accession record.
We'd like to thank the International Chimpanzee
Sequencing and Analysis Consortium, Washington
University at St. Louis School of Medicine Genome Sequencing
Center, and the Broad Institute for providing this assembly.
We'd also like to acknowledge the UCSC team who worked on
this release: Hiram Clawson, Greg Roe, and Donna Karolchik.
The chimpanzee browser annotation tracks were generated by
UCSC and collaborators worldwide.
19 January 2011 - Browser Released for Zebrafish Zv9 Assembly
The most recent zebrafish assembly -- Zv9 (UCSC version
danRer7, Jul. 2010) -- is now available in the UCSC
Genome Browser. This assembly was produced by
The Wellcome Trust Sanger Institute, UK.
The Zv9 assembly comprises a sequence length of 1.4 Gb in
26 chromosomes and 1,107 scaffolds. This assembly is based
on a clone path sorted with
the high-density meiotic map SATMAP (Clark et al., in
preparation). The data freeze was taken on 1 April 2010.
The remaining gaps were filled with sequence from WGS31, a
combined Illumina and capillary assembly. The assembly
integration process involved sequence alignemnts as well as
cDNA, marker and BAC/Fosmid end sequence placements.
The zebrafish mitochondrial sequence is also available in
the Genome Browser as the virtual chromosome, chrM. For
more details about the Zv9 assembly, see the Sanger
Institute page for the
Danio rerio Sequencing Project.
The danRer7 sequence and annotation data can be
downloaded from the UCSC Genome Browser
FTP server
or
downloads
page. Please review the Sanger Institute
guidelines for using these data.
We'd like to thank the Wellcome Trust Sanger Institute
for providing this assembly.
The UCSC zebrafish Genome Browser
was produced by Hiram Clawson, Greg Roe, Mary Goldman,
Brian Raney and Donna Karolchik. See the
credits
page for a detailed list of the organizations and
individuals who contributed to this release.
10 January 2011 - Introducing Genome Browser Right-click Navigation
Several of the common display and navigation operations
offered on the Genome Browser tracks page may now be quickly
accessed by right-clicking on a feature on the tracks image
and selecting an option from the displayed menu. Depending
on context, the right-click feature will let you
change the track display mode, zoom in or out to the exact
position coordinates of the feature, open the "Get
DNA" window at the feature's coordinates, display
details about the feature, open a popup window to configure
the track's display, or display the entire tracks image in
a separate window for inclusion in spreadsheets or other
documents. (Note that the "PDF/PS" option in the
Genome Browser top navigation bar can also be used to
generate a high-quality annotation tracks image suitable
for printing.)
To use the right-click feature, make sure the "Enable
advanced javascript features" option on the
tracks
configuration page is checked, and configure your
internet browser to allow the display of popup windows from
genome.ucsc.edu. When enabled, the right-click
navigation feature replaces the default contextual menu
typically displayed by your internet browser when you
right-click on the tracks image. A few combinations of the
Mozilla Firefox browser on Mac OS do not support the
right-click menu functionality using secondary click; in
these instances, you must use the explicit ctrl-click action
to display the menu.
Credit goes to Larry Meyer and Brooke Rhead for doing the
lion's share of the design, development and testing of this
feature, with engineering support from Tim Dreszer and
additional testing by several others on the QA team.
2 December 2010 - Searching for Tracks Just Got Easier!
The number of genome assemblies and annotation
tracks in the UCSC Genome Browser has increased
exponentially over the past few years. Along with this
growth, it has become more difficult for browser users to
sort through the many tracks to find the data they're
interested in.
With our latest Genome Browser release, we've introduced a
new track search feature that will help you to quickly and
easily find and display specific annotation data sets. The
search feature is available via the "track search" button
on the browser gateway and tracks display pages.
The default search takes one or more terms as input, and
returns a list of all the browser tracks in which the name,
description, group or associated metadata contains the
terms. The advanced search option lets the user fine-tune
the search based on the track name, description, and group.
Individuals interested in the ENCODE data available on
selected human genome assemblies can use the advanced
search to specify particular ENCODE metadata terms, such
as cell line, experiment type, etc.
Once the list of search results is shown, you may choose
which tracks you'd like to view in the browser, and can
adjust the display modes. The search results list is
sortable by multiple criteria, and provides direct links
to detailed track descriptions and additional information
about the tracks.
Special thanks to Tim Dreszer and Larry Meyer for
implementing track search, and to the QA team
for their work in testing and finetuning it. We hope our
users, particularly those exploring ENCODE
data, will take advantage of this new feature. As always,
we appreciate your feedback. Please send comments or
questions to
genome@soe.ucsc.edu.
24 August 2010 - New Drag and Reorder Functionality Released
We are pleased to announce new functionality in the Genome Browser. It is now
possible to rearrange the order that tracks appear in the browser image
directly from the browser image itself. To reorder tracks, click-and-hold the
side label or gray mini-button of a single track and drag the highlighted track to a new
position within the image.
Because reordering is now available in the browser image itself, we have
removed the "enable track reordering" option from the configuration page.
Thanks to Tim Dreszer and the rest of the team for implementing and testing this feature.
20 August 2010 - New ENCODE Integrated Regulation Super-track Released
We are pleased to announce the release of the ENCODE Integrated
Regulation super-track, a collection of regulatory tracks containing
state-of-the-art information about the mechanisms that turn genes on and
off at the transcription level. Individual tracks within the set show
enrichment of histone modifications suggestive of enhancer and promoter
activity, DNAse clusters indicating open chromatin, regions of
transcription factor binding, and transcription levels. When viewed in
combination, the complementary nature of the data within these tracks
has the potential to greatly facilitate our understanding of regulatory
DNA.
The data comprising these tracks were generated from hundreds of
experiments on multiple cell lines conducted by labs participating in
the Encyclopedia of DNA Elements (ENCODE) project, and were submitted to
the UCSC ENCODE Data Coordination Center for display on the Genome
Browser.
Faced with the problem of how to display such a large amount of data
in a manner facilitating analysis, UCSC has developed new visualization
methods that cluster and overlay the data, and then display the
resulting tracks on a single screen. Each of the cell lines in a track
is associated with a particular color. Light, saturated colors are used
to produce the best transparent overlay.
The data in the ENCODE Regulation super-track, as with all data from the
production phase of the ENCODE project, have genome-wide coverage. In
general, Genome Browser tracks that show ENCODE-generated data can be
identified by the double-helix icon preceding the name in the track
list. Currently, the ENCODE Regulation data are available only on the
March 2006 (NCBI Build 36, UCSC version hg18) assembly of the human
genome.
For a detailed description of the datasets contained in this super-track
and a discussion of how the tracks can be used synergistically to
examine regions of regulatory functionality within the genome, see the
track description page.
18 August 2010 - Cat Genome Browser Available
We have released a Genome Browser for the latest assembly of Cat (Felis catus).
The GTB V17E assembly (December 2008, UCSC version felCat4) was produced by the NHGRI
Genome Technology Branch and NIH Intramural Sequencing Center, Maryland; Agencourt
Bioscience Corporation, Massachusetts; NCI Laboratory of Genomic Diversity, Maryland;
and Hill's Pet Nutrition, Inc, Kansas. The mitochondrial genome was sequenced by NCI
Laboratory of Genomic Diversity. For detailed sequencing and assembly information, see
the NCBI Felis catus
assembly page.
Downloads of the Cat data and annotations may be obtained from the
UCSC FTP site
or
Downloads
page. These data have been freely provided for use in the UCSC Genome Browser
with specific conditions for use.
Many thanks to NHGRI, Agencourt Bioscience Corporation, NCI and Hill's Pet Nutrition
for providing these data. The felCat4 annotation tracks were generated by UCSC and
its collaborators. We'd also like to acknowledge the UCSC Cat browser team: Chin Li,
Antonio Coelho, Mary Goldman and Donna Karolchik. See the
Credits
page for a detailed list of the organizations and individuals who contributed to
this release.
23 July 2010 - BigBed/BigWig Paper Published
Last summer, we announced the release of new data formats for very large data sets: BigBed
and BigWig. Read more about these data formats
here. As a follow up, we are pleased to announce that we have published a
paper on these new file formats.
From the abstract:
BigWig and BigBed files are compressed binary indexed files containing data at several
resolutions that allow the high-performance display of next-generation sequencing experiment
results in the UCSC Genome Browser. The visualization is implemented using a multi-layered
software approach that takes advantage of specific capabilities of web-based protocols and
Linux and UNIX operating systems files, R trees, and various indexing and compression tricks.
As a result, only the data needed to support the current browser view is transmitted rather
than the entire file, enabling fast remote access to large distributed data sets.
The supplemental materials (available online) contain the technical details about the
implementation.
21 July 2010 - Free Genome Browser
workshops available
In the years since its introduction, the UCSC Genome Browser has
become an important tool for research and teaching. As it has grown
in capacity and therefore complexity, however, even experienced users
sometimes have
difficulty leaning how to make the most of it.
We plan to
provide a limited number free browser training workshops at selected
institutions during the coming year.
We invite you to apply.
Please indicate your
interest by completing our survey:
Apply for free workshop
15 July 2010 - Conservation
track available for zebrafish (danRer6)
We are pleased to announce the release of a new Conservation track based on the
zebrafish (danRer6) assembly. This track shows multiple alignments of 6
vertebrate species and measurements of evolutionary conservation using phastCons
from the PHAST package. The multiple alignments were generated using multiz and
other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment
pipeline. Conserved elements identified by phastCons are displayed in the
companion "Most Conserved" track.
Top graph: total traffic on the UCSC
domain during June-July, 2000. Bottom graph: page hit
statistics on genome.ucsc.edu in the
ensuing years since the Genome Browser was released.
UCSC is pleased to celebrate the 10-year anniversary of the
debut of the first assembled human genome sequence and its
then-fledgling visualization tool, the UCSC Genome Browser.
Released on July 7, 2000, the genome sequence instantly
created unprecedented web traffic on the
ucsc.edu domain as researchers around the world
scrambled to download the data: 0.5 terabytes per day, a
record that stood for many years.
David Haussler recounts that day:
"Seeing the waterfall of As, Gs, Cs, and Ts pouring
off our server was an emotional moment. We were witnessing
the product of more than three billion years of evolution,
sequences passed down from the beginning of life to
present-day humans." 1
The UCSC Genome Bioinformatics group is proud of the role
we have played in bringing the
human genome, as well as the genomes of many other species,
to the world. We'd like to thank NHGRI, HHMI, and our other
funding agencies for making this service possible, and
also our many users and collaborators for their suggestions,
contributions, and support throughout the years. We look
forward to serving as a reliable
source of bioinformatics tools and genomic annotations in
the years to come while facing the exciting challenges
presented by rapidly advancing technology.
To read more about UCSC's role in the race to assemble the
first working draft of the human genome, including Jim
Kent's remarkable programming feat that pulled it all
together in the final weeks, see the
Center for Biomolecular Science and
Engineering (CBSE) website.
(1) Sansom C, Morrison McKay BJ (2008) ISCB Honors David Haussler and Aviv
Regev. PLoS Comput Biol 4(7): e1000101
4 June 2010 - dbSNP 131 Available for hg19
We are pleased to announce the release of dbSNP build 131,
available from on the human
assembly (GRCh37/hg19). The dbSNP build 131 is available
at NCBI.
The SNPs (131) track contains 26,033,053
mappings of 23,445,889 reference SNPs that have been mapped to the
reference genome by dbSNP. This is a significant increase from the
provisional hg19 mappings of build 130 (18,404,149 mappings of
17,512,501 SNPs).
You will find the SNPs (131) track on the Human Feb. 2009
(GRCh37/hg19) browser in the "Variation and Repeats" group.
Many thanks to dbSNP at NCBI for the data. The track was
produced at UCSC by Angie Hinrichs and Mary Goldman.
3 June 2010 - Updated Marmoset Genome Browser Available
We have released an updated marmoset (Callithrix
jacchus) assembly, UCSC version calJac3, corresponding
to the March 2009 v3.2 assembly from the Genome
Center at Washington University St. Louis School of
Medicine (WUSTL).
This draft of the marmoset genome has approximately 6X
coverage. For statistics and details on the assembly
process, see the WUSTL Callithrix jacchus
assembly information page.
Bulk downloads of the sequence and annotation data are
available via the Genome Browser
FTP
server or the
Downloads
page. See the WUSTL Genome Center's
data use policy for conditions of use.
Many thanks to the Genome Center at WUSTL School of
Medicine for providing the assembly data.
The calJac3 annotation tracks were generated by UCSC and
collaborators. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
12 May 2010 - Pig Genome Browser Released
We have released a Genome Browser for the pig, Sus scrofa.
This assembly (SGSC Sscrofa9.2
(NCBI project 10718,
GCA_000003025.2)) was produced by the
Swine Genome Sequencing Consortium and the
Wellcome Trust Sanger Institute.
The pig is a member of the artiodactyls
(cloven-hoofed mammals),
which is an evolutionary clade distinct from the primates and
rodents. It is an important model for human health, particularly
for understanding complex traits such as obesity and cardiovascular
disease. There is extensive conserved homology with the human genome.
The pig genome assembly is a hybrid of BAC end-sequencing to anchor
contigs combined with whole-genome shotgun (WGS) libraries. There
are 19 chromosomes: chr1 - chr18, chrX and the mitochondrial sequence
chrM (GenBank accession number NC_012095) for a total sequence length of
2,262,501,571 bases. There are 31,203,023 'N' bases in gaps, leaving
2,231,298,548 ACGT bases. For more information, see the
Sanger Institute's Porcine Genome Sequencing Project
web page.
Many thanks to the Swine Genome Sequencing Consortium and the
Wellcome Trust Sanger Institute for the pig assembly data.
Bulk downloads of the sequence and annotation data are
available via the Genome Browser
FTP server
or the Downloads
page. These data have specific
conditions for use.
The pig browser annotation tracks were generated by UCSC
and collaborators worldwide. The UCSC Pig browser was produced
by: Hiram Clawson, Brian Raney, Mark Diekhans, and Mary
Goldman. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
6 May 2010 - UCSC Hosts Portal for Neandertal Sequence, Alignments, and Analyses
In conjunction with the publication of the paper Green
et al.A Draft Sequence of the Neandertal Genome
in the May 7 issue of Science, the UCSC
Genome Browser project has released a public
Neandertal portal that may be
used to access the Neandertal sequence, alignments to
the UCSC hg18 (NCBI Build 36) human reference assembly and
the UCSC panTro2 (Chimpanzee Sequencing and Analysis
Consortium v2.1) chimpanzee reference assembly, and
several associated analyses.
Neandertals are the closest extinct relatives of humans.
They lived in much of Europe and western Asia before
disappearing from the fossil records approximately
30,000 years ago.
The Neandertal genome sequence consists of short sequence
fragments, usually about 50 base pairs long, mapped to the
human reference genome. The sequence was
derived primarily from DNA extracted from
three Neandertal bones, each about 40,000 years old, found
in the Vindija Cave in Croatia; smaller amounts of data were
also obtained from three bones from other sites. The bulk
sequencing was carried out on the Illumina GAII platform.
Neandertal DNA was differentiated from the background of
microbial sequences in the bone by similarity to the human
or chimpanzee genomes.
The draft sequence of the Neandertal genome yields
important new insights into the evolution of modern humans.
Among the findings discussed in the Science
publication is evidence that some early modern
humans, after their migration out of Africa, interbred with
Neandertals, resulting in traces of Neandertal DNA
sequences in the genomes of present-day non-Africans. The
authors also cataloged genetic features unique to modern
humans by comparing the Neandertal, human, and chimpanzee
genomes. Among the genes highlighted in the study as
likely to have undergone important changes in recent human
evolution are those involved in cognitive development,
skull structure, energy metabolism, skin morphology and
physiology.
We'd like to thank Richard Green (formerly of the Max-Planck
Institute, and now an assistant professor of
biomedical engineering at UCSC) and the many authors
of the Science paper for providing the UCSC Genome
Browser with these data. We'd also like to acknowledge the
hard work of the UCSC Genome Browser staff who pulled
together the annotations and information for the UCSC
Neandertal portal: Angie Hinrichs, Katrina Learned, and
Pauline Fujita.
26 Apr. 2010 - European Rabbit Genome Browser Released
We have released a Genome Browser for the European
rabbit, Oryctolagus cuniculus. This assembly
(UCSC version oryCun2, Broad oryCun2) was produced
by the Broad Institute of MIT and Harvard, Cambridge, MA.
The European rabbit is the precursor of all domestic rabbits. It is a valuable model
in both immunology and evolutionary biology.
The genome has been sequenced to nearly 7.5X coverage.
The sequence is 2.7 Gb in length and includes 21 autosomes, the X chromosome,
and the mitochondrial DNA (chrM), as well as 3,219 unplaced segments.
For more information on the assembly, see the
Rabbit Genome Project page.
Many thanks to the Broad Institute for the rabbit assembly
data. The oryCun2 annotation tracks were generated by UCSC
and collaborators. We'd also like to acknowledge the UCSC Rabbit browser
team: Hiram Clawson and Antonio Coelho. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
16 Apr. 2010 - Giant Panda Genome Browser Released
We have released a Genome Browser for the giant
panda, Ailuropoda melanoleuca. This assembly
(UCSC version ailMel1, BGI AilMel1) was produced
by the Beijing Genomics Institute at Shenzhen, Shenzhen, China. The
panda is a member of Ursidae, despite earlier taxonomy that marked it as a relative
of the raccoon. It has become the most recognized symbol
for the fight for animal conservation.
This draft of the panda genome has a size of
approximately 2.3 Gb at 94% coverage. The assembly
comprises 81,467 scaffolds and chrM (mitochondrial DNA).
For more information on the assembly, see the
BGI Giant Panda Database page.
Many thanks to the Beijing Genomics Institute at Shenzhen for the panda assembly
data. The ailMel1 annotation tracks were generated by UCSC
and collaborators. We'd also like to acknowledge the UCSC Panda browser
team: Hiram Clawson, Ann Zweig, and Antonio Coelho. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
24 Mar. 2010 - African Savannah Elephant Genome Browser Released
We have released a Genome Browser for the African
savannah elephant, Loxodonta africana. This assembly
(UCSC version loxAfr3, Broad loxAfr3) was produced
by the Broad Institute, Cambridge, MA, USA. The
elephant was the first member of Afrotheria to be sequenced. Afrotheria
is the deepest node of Eutheria, and the elephant sequence should be
useful in reconstructing the ancestral eutherian genome.
This draft of the elephant genome has a size of
approximately 3 Gb with 7X coverage. The assembly
comprises 2352 scaffolds and chrM (mitochondrial DNA).
For more information on the assembly, see the Broad
Institute
Elephant Genome Project page.
Many thanks to the Broad Institute for the elephant assembly
data. The loxAfr3 annotation tracks were generated by UCSC and collaborators. We'd also like to acknowledge the UCSC Elephant browser
team: Hiram Clawson, Pauline Fujita, Vanessa Swing, Antonio Coelho, and Donna Karolchik. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
19 Mar. 2010 - California Sea Hare Genome Browser Released
We have released a Genome Browser for the California
sea hare, Aplysia californica. This assembly
(UCSC version aplCal1, Broad version Aplcal2.0) was produced
by the Broad Institute, Cambridge, MA, USA. The
sea hare is the first mollusc to be sequenced, and is
particularly noted for its nervous system, which is quite
useful for neurobiological experimentation.
This draft of the sea hare genome has a size of
approximately 712 Mb with nearly 10X coverage. The assembly
comprises 8766 scaffolds and chrM (mitochondrial DNA).
For more information on the assembly, see the Broad
Institute
Aplysia Genome Project page.
Many thanks to the Broad Institute for the sea hare assembly
data. The aplcal1 annotation tracks were generated by UCSC
and collaborators. We'd also like to acknowledge the UCSC Sea Hare browser
team: Galt Barber, Brian Raney, Hiram Clawson, Katrina Learned, Antonio Coelho,
and Donna Karolchik.
See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
12 Mar. 2010 - Updated Tetraodon Genome Browser Available
We have released a Genome Browser for the latest assembly
of Tetraodon nigroviridis. The V8 assembly
(March 2007, UCSC version tetNig2) was provided by
Genoscope, Evry, France, in collaboration
with the
Broad Institute, Cambridge, MA, USA.
For detailed sequencing and assembly information, see the
Genoscope Tetraodon nigroviridisassembly page.
Downloads of the Tetraodon data and annotations may be
obtained from the UCSC
FTP site or
Downloads page.
These data have been freely provided by Genoscope for use
in the UCSC Genome Browser with
specific conditions for use. For more
information about the Tetraodon nigroviridis
project, see the Genoscope
website.
Many thanks to Genoscope and the Broad Institute for
providing these data. The tetNig2 annotation tracks were
generated by UCSC and its collaborators. We'd also like to
acknowledge the UCSC Tetraodon browser team, which includes
several new faces: Hiram Clawson, Mark Diekhans, Brian
Raney, Ann Zweig, Mary Goldman, Vanessa Swing, Antonio
Coelho, Robert Kuhn, and Donna Karolchik.
See the
credits
page for a detailed list of the organizations and
individuals who contributed to this release.
24 Feb. 2010 - New Gene Name Search Functionality Released
UCSC has introduced a new gene search functionality in the
Genome Browser, available through a "gene" text
box on the gateway and annotation tracks
pages. If you are searching for a particular gene, but
you don't remember the exact coordinates, simply type
the gene name into the box. The software will suggest
gene names as you type; you can either choose a gene
from the list, or finish typing your full gene name
and then press "jump" or hit enter.
This functionality is available now—there's
nothing to configure. Start using it
here.
Thanks to Larry Meyer and the rest of the team for
implementing and testing this feature.
We are pleased to announce the availability of another new
track type for
Custom Tracks: the Binary Alignment/Map
(BAM).
BAM is the compressed binary version of the
Sequence Alignment/Map (SAM)
format, a compact and index-able representation of
nucleotide sequence alignments. Many next-generation
sequencing and analysis tools work with
SAM/BAM. For custom track display, the main advantage of
indexed BAM over PSL and other human-readable alignment
formats is that only the portions of the files needed to
display a particular region are transferred to UCSC.
This makes it possible to display alignments from files that
are so large that the connection to UCSC would time out
when attempting to upload the whole file to UCSC. Both the i
BAM file and its associated index file remain on your
web-accessible server (http or ftp), not on the UCSC server.
UCSC temporarily caches the accessed portions of the files
to speed up interactive display.
13 Jan. 2010 - Lifespan of Custom Tracks within Sessions
Due to the popularity of UCSC
custom tracks
and
sessions,
we are running out of disk space for storing custom
tracks accessed within sessions. Although sessions
themselves are saved for one year, user-generated tracks
within sessions (including custom tracks) are saved for 48
hours, the typical period for other custom tracks. Until
now, because we have had space available on the server, we
have attempted to keep custom tracks alive for the lifetime
of the session.
While we provide short-term custom track storage as a
service to users who want to view their own data in the
UCSC Genome Browser, we unfortunately do not have the
resources to guarantee long-term data storage.
Over the next few days, we will begin to actively delete
custom tracks within sessions that have not been accessed
within the past four months. If you actively use your
custom tracks within saved sessions, they will not be
deleted.
Instead of uploading your data to our servers, please
consider using alternate data types such as
bigBed,
bigWig,
or other URL-based tracks that enable you to store your
data locally.
11 Jan. 2010 - Zebrafish release zv8 now available in Genome Browser
The most recent zebrafish assembly -- zv8 (UCSC version
danRer6, Dec. 2008) -- is now available in the UCSC
Genome Browser. This assembly was produced by
the Wellcome Trust Sanger Institute, UK.
The danRer6 assembly consists of nearly 1.5 billion bp in
11,623 scaffolds with a coverage of 6.5-7x. It includes
sequence anchored to chromosomes
1-25 and chrM (mitochondrial), as well as 11,418 unplaced
scaffolds. Significant problems existing in previous
assemblies have been rectified in this assembly through the
use of a whole-genome shotgun assembly with more coverage
and a reorganization of the fingerprint contig order and
orientation through more careful use of maps.
For more information about this assembly, see the Sanger
Institute web page for the
Danio rerio Sequencing Project
and the track description page for the danRer6 Assembly
track.
The danRer6 sequence and annotation data can be
downloaded from the UCSC Genome Browser
FTP server
or
downloads
page. Please review the
guidelines for using these data.
We'd like to thank the Wellcome Trust Sanger Institute
for providing this assembly.
The UCSC zebrafish Genome Browser
was produced by Galt Barber, Robert Kuhn, Katrina Learned,
and Donna Karolchik. The initial set of annotation tracks
was generated by the UCSC Genome Bioinformatics Group. See
the
credits
page for a detailed list of the organizations and
individuals who contributed to the release of
this browser.
14 Dec. 2009 - New job posting: Biological Data Technician
The UCSC Genome Browser project is looking for a
bioinformatician, biologist, or software engineer with a
strong biology background to collect and import data
into the UCSC Genome Browser database and
website. This person will work closely with external
research laboratories to capture their experimental results
and methods and with internal software developers and
database testing staff to make the data accessible to the
worldwide scientific community.
Candidates must have a bachelor's degree in bioinformatics
or a biological science (or equivalent experience), be
proficient in UNIX/Linux command-line use, competent in
UNIX shell scripting and Perl programming,
and familiar with relational database concepts and SQL.
Besides having the ability to quickly learn and interpret
biological and technical information, the ideal candidate is
an effective communicator, resourceful, and a diplomatic
team player who is both quality-oriented and able to work
effectively under deadline.
To find more information and application instructions for
this job as well as other open positions with the UCSC
Genome Browser project and the UCSC Center for Biomolecular
Science and Engineering, see the CBSE
staff positions web page.
7 Dec. 2009 - Human Genome Browser default changing to hg19
In conjunction with the release of the UCSC Genes and
Conservation tracks on the hg19 (GRCh37) human assembly,
we have changed the default human browser on our website
from hg18 to hg19. In general, if you are currently using
the hg18 (or older) browser, the
Genome Browser will continue to display that assembly for
you when you start it up. However, there are circumstances
in which the assembly may switch to the newer version (for
instance, if you reset your browser defaults). If you find
yourself in a situation where some of your favorite browser
tracks have "disappeared", you may want to check that
you're viewing the right assembly.
1 Dec. 2009 - New UCSC Genes and Conservation tracks released on hg19 browser
We're happy to announce the release of two of our most
popular data sets on the hg19/GRCh37 human Genome Browser.
The UCSC Genes track is a moderately conservative
set of gene predictions based on data from RefSeq, Genbank,
CCDS and UniProt. The Conservation track shows
multiple alignments of 46 vertebrate species and
measurements of evolutionary conservation using two methods
(phastCons and phyloP) from the PHAST package for all
vertebrate species as well as primate and placental mammal
subsets. For more information about these annotations, read
the description pages that accompany these tracks.
The UCSC Genome Browser project is currently accepting
applications for a Biological Database Testing/User Support
Technician (Programmer/Analyst I).
We are looking for a talented self-motivated individual who
would like to use their skills in computer science,
biology, and bioinformatics on a fast-paced project
featuring the work of top genomics scientists worldwide.
For a summary of the position details and qualifications,
see
Biological Database Testing/User Support
Technician on the Center for Biomolecular Science and
Engineering (CBSE) website. For detailed job descriptions
and application information, go to the
UCSC Staff
Employment website, click the "Search
Postings" link on the sidebar, and type in job
#0902365 (Testing/User Support Technician).
9 September 2009 - Changes to the bigBed/bigWig data formats
If you have been taking advantage of the new bigBed format
(for very large data sets), you'll be happy to hear that we
have considerably slimmed down the memory footprint of the
program that converts BED files into bigBed files: bedToBigBed.
Because it now uses a multi-pass approach, it now takes only
1/4 the amount of RAM as the size of the uncompressed BED input
file (instead of the 5x RAM it needed previously!). Read more
here.
Pick up the new bedToBigBed executable
here.
In conjunction with this change, there is also a change to the
way you must specify your bigBed or bigWig custom track. When
you specify the location of your local bigBed/bigWig file (on
your web-accessible http, https, or ftp server), use the
designation "bigDataUrl" instead of the old
"dataUrl":
track type=bigBed name="My Big Bed" description="Some Data from My Lab"
bigDataUrl=http://myorg.edu/mylab/myBigBed.bb
Additionally, we would like to announce a companion program to
the previously-announced wigToBigWig program: bedGraphToBigWig.
This program converts bedGraph files into bigWig files. The
bedGraph format allows display of sparse or varying-size data.
Read more
here.
You can download the new bedGraphToBigWig utility
here.
The main advantage of the bigBed and bigWig formats is that
only the portions of the files needed to display a particular
region are transferred to UCSC, so for large data sets,
displaying bigBed/bigWig data is considerably faster than
regular BED/wig data. The bigBed/bigWig file remains on your
web accessible server (http, https, or ftp), not on the UCSC
server. Consequently, creating your custom track is very fast.
Only the portion that is needed for the chromosomal position you
are currently viewing is locally cached at UCSC as a
"sparse file".
10 August 2009 - Updated Yeast Genome Browser Released
The S288C strain was used in this sequencing project. Reference
information for each chromosome may be found in the SGD
Systematic Sequencing Table.
Bulk downloads of the sequence and annotation data are
available via the Genome Browser
FTP server
or the Downloads
page.
See the Credits
page for details on contributions to this release.
22 July 2009 - Updated Opossum Genome Browser Released
We have released an updated opossum (Monodelphis domestica)
genome browser, UCSC version monDom5, corresponding to the
Broad Institute's October 2006 assembly.
This draft of the opossum genome has approximately 6.8X
coverage. The assembly length is nearly 3.61 billion bp
including gaps (3.50 billion bp without gaps) contained on
chromosomes 1-8, X, M (mitochondrial DNA), and Un (unmapped
clone contigs). The N50 of the scaffolds including gaps is
60,456 kb; the N50 without gaps is 110 kb.
Many thanks to The Broad Institute for the opossum assembly
data. The monDom5 annotation tracks were generated by UCSC
and collaborators worldwide. See the
Credits
page for a detailed list of the organizations and individuals
who contributed to this release.
7 July 2009 - Engineering Job Opening with UCSC Genome Browser Project
The UCSC Center for Biomolecular Science and Engineering is
currently accepting applications for a full-time,
experienced engineer to develop software and databases for
the UCSC Genome Browser and related projects. The
successful candidate must be independent, articulate,
self-motivated, able to learn and integrate technical
information quickly, and have a strong commitment to
quality and best engineering practices.
27 May 2009 - Australasian Genome Browser Mirror Available
We are pleased to announce the availability of a public
Genome Browser mirror for the Australasian research
community:
https://ucsc.genome.edu.au/
The Queensland Facility for Advanced Bioinformatics (QFAB),
in conjunction with the University of Queensland, Australia,
maintains this full mirror of the UCSC Genome Browser, which
is sponsored by the Australian Research Council. The QFAB
mirror offers alternative access to the Genome Browser data
when the UCSC site is unavailable, and may provide better
performance for our Australasian users.
We'd like to extend our thanks to QFAB for providing and
maintaining this mirror, and in particular to Jeremy Barker
and Michael Pheasant for their collaborative work with UCSC
in setting up this site.
27 April 2009 - New Human Browser Released
We are pleased to announce the release of the February 2009
human genome browser, UCSC version hg19.
Starting with this assembly, the human genome sequence is
now provided by the
Genome Reference Consortium, whose goal is
to correct the small number of regions in the reference that
are currently misrepresented, to close as many remaining
gaps as possible and to produce alternative assemblies of
structurally variant loci when
necessary. The hg19 browser corresponds to GRCh37.
Statistics for the GRCh37 build assembly can be found on
the NCBI
Build 37.1 Statistics web page.
The UCSC staff responsible for producing the initial hg19
browser include Hiram Clawson,
Brooke Rhead, Pauline Fujita, Ann Zweig, Katrina Learned,
and Robert Kuhn. See the
Credits page for a detailed list of the organizations and
individuals who contributed to this release.
20 March 2009 - Two Research Scientist Positions Open
The Center for Biomolecular Science & Engineering (CBSE)
invites applications from outstanding PhD- or MD-level
scientists for two distinct positions.
Position is open until filled, but applications received
after March 27 may not be considered.
Cancer Genomics Director
We seek an independent, creative scientist with cancer
research experience to guide the group in building our
cancer genomics data analysis platform into an essential
tool for cancer research and an engine for personalized,
genome-based cancer treatment. The successful candidate will
extend our existing cancer research collaborations,
conceptualize new research directions, oversee their
implementation by our outstanding postdoctoral students and
scientific programming staff, write papers and present
results at scientific meetings, and apply for additional
grants. Our exceptional collegiality and interdisciplinary
collaborations make UCSC an excellent environment for an
innovative scientist who can benefit from and contribute to
the rapid growth in the sciences and engineering at UCSC.
Read more.
Medical Genomics Director
We seek an independent, creative scientist who can guide
the group in the direction of clinical diagnostics,
pediatric/prenatal diagnostics, personalized medicine,
pharmacogenomics, or related fields, building on the
exceptional genome analysis resources at UCSC. The
successful candidate will interface with the medical
community, conceptualize genomics projects, oversee
implementation by the scientific programming staff, write
papers describing the projects, and apply for grants to
fund future projects. Our exceptional collegiality and
interdisciplinary collaborations make UCSC an excellent
environment for an innovative scientist who can benefit
from and contribute to the rapid growth in the sciences and
engineering at UCSC. Read more.
13 March 2009 - ENCODE DCC data available
We'd like to invite everyone to explore UCSC's
ENCODE Data
Coordination Center website, as well as the ENCODE data
displayed as annotation tracks in the UCSC Genome Browser.
Today's
featured
dataset is a track showing transcription factor
binding sites determined by ChIP-seq, produced through a
collaboration of Yale University, University of CA Davis,
and Harvard University. Many more tracks from the Feb. 2009
and Dec. 2008 ENCODE data freezes will become available
on the UCSC Genome Browser in upcoming weeks. To monitor
the ENCODE data releases in the Genome Browser, see the
UCSC ENCODE
data release page.
17 February 2009 - Navigate with drag-and-zoom
We would like to announce the release of a new navigation
feature, called drag-and-zoom, in the Genome Browser. It is
now possible to position your mouse over a location in the
Base Position track, at the top of the browser image and
define a zoom range by moving the mouse to a second place
within the image. The browser will redraw at the new
coordinates when the mouse button is released.
12 February 2009 - v200 code release on Darwin's 200th birthday
As coincidence would have it, we are releasing version 200
of the browser code base this week. Though we typically
release code on a Friday, we couldn't resist the impulse to
release a day early, on the 200th birthday of Charles
Darwin, whose ground-breaking work set the stage for modern
biology.
5 February 2009 - NHGRI Solicits Genome Sequencing Input
The National Human Genome Research Institute (NHGRI) seeks
community comments on the future of its large-scale genome
sequencing program. To stimulate discussion, NHGRI has
produced a white paper, "The Future of Genome Sequencing".
If you'd like to review the paper or would like more
information on NHGRI's long-range planning process, please
visit their planning website.
30 January 2009 - 44-vertebrate Conservation Track Available
We are pleased to announce the release of a new
Conservation track based on the human (hg18) assembly.
This track shows multiple alignments of 44 vertebrate
species and measurements of evolutionary conservation using
two methods (phastCons and phyloP) from the PHAST package,
for all species (vertebrate) and two subsets (primate and
placental mammal). The multiple alignments were generated
using multiz and other tools in the UCSC/Penn State
Bioinformatics comparative genomics alignment pipeline.
Conserved elements identified by phastCons are also
displayed in this track. For more details, visit the
track
description page.
This track is now the default Conservation track for the
hg18 human assembly. It replaces the previous 28-vertebrate
Conservation track, which is now available as
the "28-Way Cons" track.
Many people contributed to the creation of this track
including, but not limited to:
Adam Siepel (Cornell University): phastCons, phyloP,
and other programs in the PHAST package
Webb Miller, Bob Harris and Minmei Hou (Penn State
University Bioinformatics Group): blastz and multiz
Hiram Clawson, Tim Dreszer, Brian Raney, Kate
Rosenbloom and Ann Zweig (UCSC Genome Browser team)
3 December 2008 - Updated Horse Genome Browser Available
The Sep. 2007 EquCab2 release of the horse genome (Equus
caballus) is now available in the UCSC Genome Browser. This
assembly, UCSC version equCab2, was produced by the
Broad
Institute.
The horse draft genome has been sequenced to 6.8X coverage.
Approximately 84% of the sequence has been anchored to
chromosomes, which include autosomes 1-31 and sex
chromosome X. Unanchored contigs that could not be
localized to a chromosome have been concatenated into the
virtual chromosome "chrUn", separated by gaps of
1,000 bp. The mitochondrial sequence is also available in
the Genome Browser as the virtual chromosome
"chrM".
For more details about the current assembly, see
the Broad Institute
Horse Genome Project page.
The UCSC Horse Genome Browser was produced by Larry Meyer,
Hiram Clawson, Pauline Fujita, Brooke Rhead, and Donna
Karolchik. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
7 November 2008 - Medaka Genome Browser Updated
We have updated the initial UCSC Medaka Genome Browser
(oryLat1) to correct an error with chrUn in which the gap
relationships between the contigs within their
ultracontigs were incorrect. This error was introduced by
UCSC during the browser assembly process. The corrected
replacement browser, oryLat2 (Oct. 2005), is based on the
same v1.0 assembly produced by the National Institute of
Genetics (NIG) and the University of Tokyo, Japan. We
have removed the original oryLat1 assembly from the
browser.
17 September 2008 - Seven Assemblies Archived:
We have archived seven older assemblies of the human
(hg15), mouse (mm5, mm6), rat (rn2), C. elegans
(ce1), zebrafish (danRer2), and cow (bosTau1) genomes.
You can continue to download these assemblies from the
Genome Browser
downloads
server. At least two later assemblies for each of these organisms
remain available on the main Genome Browser site.
We do not provide blat servers or updated GenBank data for
archived assemblies. However, it is still possible to lift
coordinates between these assemblies and those on the main
browser site.
15 September 2008 - Request for Input on ENCODE Data Release Plan
The National Human Genome Research Institute (NHGRI)
has updated the data release plan for the
ENCODE and model organism ENCODE
(modENCODE) projects.
Because the plan is intended to take
into account the needs and responsibilities of the resource
users, NHGRI is soliciting feedback on the proposal from the
research community before the plan is finalized. To
facilitate this review, UCSC has made the
plan available to the community
here on our ENCODE website.
Please send comments directly to
Encode@mail.nih.gov
by Wednesday, October 15, 2008.
3 September 2008 - Updated UCSC Genes Set Released for hg18
We have released an updated UCSC Genes data set on the
latest human assembly (hg18, March 2006). The new annotation
can be found on the hg18 Genome Browser in the "Genes and
Gene Predictions" track group. The previous set of UCSC
Genes on the hg18 assembly has been renamed as Old UCSC
Genes in the same track group.
The UCSC Genes track shows gene predictions based on data
from RefSeq, Genbank, CCDS and UniProt. This is a moderately
conservative set of predictions, requiring the support of
one GenBank RNA sequence plus at least one additional line
of evidence. The RefSeq RNAs are an exception to this,
requiring no additional evidence. The track includes both
protein-coding and putative non-coding transcripts. Some of
these non-coding transcripts may actually code for protein,
but the evidence for the associated protein is weak.
Compared to RefSeq, this gene set has generally about 10%
more protein-coding genes, approximately five times as many putative non-coding genes, and about twice as many splice
variants.
The latest version of UCSC Genes explicitly incorporates
CCDS proteins in addition to the evidence included in
previous versions, as well as additional data from GenBank,
RefSeq, and UniProt. Although we have made every effort to
preserve UCSC Gene IDs across versions, some gene IDs have
changed in the new data set. In general, the ID number has
been incremented if the new version of a gene is larger
than the previous version, and a completely new ID has been
assigned in those instances where a splice site changed or
the protein-coding region shrank. However, searching on an
old discontinued ID from the previous gene set will take you
to the corresponding gene in the updated track.
Alternatively, you can check the kg3ToKg4 table directly to
find corresponding gene IDs.
The UCSC Genes set was produced by Jim Kent. Thanks to Ann
Zweig for heading up the testing of the new data set, and
to the entire Genome Browser QA team for coordinating its
release on our public site.
27 August 2008 - Zebra Finch Genome Browser Released
We've added the Jul. 2008 release of the zebra finch genome
(Taeniopygia guttata) to our collection of
vertebrate genome browsers. The v3.2.4 draft assembly
(UCSC version taeGut1) was produced by the Genome Sequencing
Center at the Washington University in St. Louis (WUSTL)
School of Medicine in St. Louis, MO, USA.
The zebra finch genome is the second bird genome to be
sequenced (following the chicken, Gallus gallus).
The DNA used for the shotgun sequencing and the BAC and
cosmid libraries was derived from a single male zebra finch.
The initial assembly was generated using PCAP with
approximately 6X coverage. About 1.0 Gb of the 1.2-Gb
genome has been ordered and oriented along 33 chromosomes
and one linkage group. The chromosome names are based on
their homologous chromosomes in the chicken (Gallus
gallus). For more assembly
details, as well as a cross reference table of
zebra finch and chicken chromosome names, see the WUSTL
assembly notes.
Bulk downloads of the sequence and annotation data are
available from the Genome Browser
FTP server
or Downloads
page. These data have
specific
conditions for use. Please refer to the WUSTL
data use policy for additional usage
guidelines and citation information.
The UCSC Zebra Finch Genome Browser and initial annotations
were produced by Brian Raney, Kayla Smith, Pauline Fujita,
and Donna Karolchik. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
22 July 2008 - Updated C. elegans Browser Released
Culminating our recent updates of the nematode browsers on
our site, we've released a Genome Browser for the latest
C. elegans assembly based on sequence version WS190
deposited into WormBase in May 2008. This new assembly
(UCSC version ce6) was produced jointly by the Wellcome
Trust Sanger Institute in Hinxton, England, and the Genome
Sequencing Center at Washington University in St. Louis
(WUSTL) School of Medicine, MO, USA. The ce6 browser
includes a Conservation annotation and pairwise alignment
tracks comparing C. elegans sequence with that of
five other worms.
Bulk downloads of the sequence and annotation data are
available via the Genome Browser
FTP
server or
Downloads
page. Please review the WUSTL
data use policy for usage restrictions
and citation information.
We'd like to thank WUSTL and the Sanger Institue for
providing the sequence data
for this assembly. The UCSC ce6 browser was produced by
Hiram Clawson, Kayla Smith, Pauline Fujita, Brooke Rhead,
and Donna Karolchik. See the Genome Browser
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
26 June 2008 - New Worm Genome Available
Along with the set of worm browser updates that we're
currently releasing, we've added a new nematode to the
collection: Caenorhabditis japonica. This genome
assembly (UCSC version caeJap1, Mar. 2008) corresponds to
the v. 3.0.2 assembly produced by the Genome Sequencing
Center at the Washington University St. Louis (WUSTL) School
of Medicine.
Bulk downloads of the sequence and annotation data are
available via the Genome Browser
FTP
server or
Downloads
page. Please review the WUSTL
data use policy for usage restrictions
and citation information.
We'd like to thank WUSTL for providing the sequence data
for this assembly. The UCSC caeJap1 browser was produced by
Hiram Clawson, Ann Zweig, and Donna Karolchik. See the
Genome Browser
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
20 June 2008 - Two Worm Updates Released
We've updated our browsers for the C.
remanei and C. brenneri nematode genomes.
Both sets of sequence were
obtained from the Genome Sequencing Center at Washington
University in St. Louis (WUSTL) School of Medicine. The
C. remanei assembly (UCSC version caeRem3)
corresponds to WUSTL version 15.0.1 dated May 2007. The
C. brenneri assembly (UCSC version caePb2) is
based on WUSTL version 6.0.1 dated Feb. 2008.
Bulk downloads of the sequence and annotation data are
available via the Genome Browser
FTP
server or
Downloads
page. Please review the WUSTL
data use policy for usage restrictions
and citation information.
We'd like to thank WUSTL for providing the sequence data
for these assemblies.
The UCSC worm browsers were produced by Hiram Clawson,
Brooke Rhead, Pauline Fujita, and Donna Karolchik.
See the Genome Browser
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
10 June 2008 - Lamprey Browser Released
We have released a Genome Browser for the Mar. 2007
assembly of the lamprey genome, Petromyzon
marinus. This assembly, UCSC version petMar1, was
produced by the Genome Sequencing Center at the
Washington University in St. Louis School of Medicine
(WUSTL), St. Louis, MO, USA.
Bulk downloads of the sequence and annotation data are
available from the Genome Browser
FTP server
or Downloads
page. The lamprey sequence is made freely available before
scientific publication. Please see the WUSTL
data use policy for usage restrictions
and citation information.
The UCSC Lamprey Genome Browser was produced by
Hiram Clawson, Ann Zweig, Pauline Fujita, and Donna
Karolchik. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
10 June 2008 - Lancelet Genome Available in Browser
The Mar. 2006 release of the lancelet genome
(Branchiostoma floridae) is now available
in the UCSC Genome Browser. This assembly, UCSC version
braFlo1, was produced by the
DOE Joint Genome Institute (JGI),
Walnut Creek, CA, USA.
Bulk downloads of the sequence and annotation data are
available from the Genome Browser
FTP server
or Downloads
page. The lancelet sequence is made freely available
before scientific publication. Please see the JGI
data release policy for usage
restrictions and citation information.
The UCSC Lancelet Genome Browser was produced by
Hiram Clawson, Ann Zweig, Pauline Fujita, and Donna
Karolchik. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
5 June 2008 - Guinea Pig Browser Released
The Feb. 2008 CavPor3 release of the guinea pig genome
(Cavia porcellus) is now available
in the UCSC Genome Browser. This assembly, UCSC version
cavPor3, was produced by the
Broad
Institute.
The guinea pig is one of 24 mammals whose genomes are being
sequenced as part of the
Mammalian Genome Project, funded
by the National Institutes of Health. While most of these
genomes are slated for low-coverage (2X), a limited subset
(including the guinea pig genome) are being sequenced to a
higher quality of 6-7X.
The guinea pig genome has been sequenced to 6.76X coverage
with 95.55% of bases assembled. A total of 3143 scaffolds
cover 2,722,377,657 bases (2.17% in gaps), with 50% of the
scaffolds having a (N50) length of at least 27,408,292
bases (not including gaps). For more details about the
assembly, see the Broad Institute
Mammmalian Genome Project page.
The UCSC Guinea Pig Genome Browser was produced by
Tim Dreszer, Kate Rosenbloom, Hiram Clawson, Kayla Smith,
Robert Kuhn, and Donna Karolchik. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
5 May 2008 - GSID HIV Data Browser Now Available
Global Solutions for Infectious Diseases (GSID) has
announced the launch of an HIV Data Browser with clinical
and viral sequence data from infected subjects in the
VAX004 (North American/European) Phase III clinical trial
of the AIDSVAX B/B vaccine. The browser, which is a
customized version of the
UCSC Genome Browser developed by the UCSC Genome
Bioinformatics group and hosted by GSID, provides
researchers with searchable demographic and clinical data
from volunteers who became HIV infected during the VAX004
trial. Using the browser, viral sequences may be aligned
with one another or with reference or consensus sequences.
GSID is making these AIDSVAX data and serological samples
available to the HIV
research community through an agreement with VaxGen and
with funding provided by the Bill and Melinda Gates
Foundation.
Future releases will include the addition of clinical and
viral sequence data from infected subjects in the VAX003
(Thai) Phase III clinical trial of AIDSVAX B/E, and
immunogenicity data from infected subjects in both the
VAX004 and VAX003 trials. The browser may be
expanded to include data from uninfected subjects in both
trials as well.
We'd like to announce the release of a Genome Browser and
Blat server for the marmoset genome (Callithrix
jacchus).
The June 2007 assembly -- WUSTL version Callithrix
jacchus-2.0.2, UCSC version calJac1 -- was produced by
Washington University St. Louis (WUSTL) School of Medicine
Genome Sequencing Center in St. Louis, MO, USA.
C. jacchus, a member of the New World
monkey clade, is the most widely studied marmoset. It is a
popular non-human primate model due to its small body size
and unique biological features, and has contributed to the
study of brain function, immunity, reproductive biology and
drug toxicity. C. jacchus marmosets typically give
birth to twins that are somatic chimeras, i.e. each sibling
is the mixture of sibling genotypes. (Excerpted from the
WUSTL C. jacchus project page.)
The C. jacchus genome was sequenced to 6X coverage
using DNA from a female marmoset provided by the
Southwestern
National Primate Research Center in San Antonio, TX, USA.
DNA from a full brother of the female was used as the source
for the CHORI-259 BAC library. This assembly is composed of
49,724 supercontigs containing a total of approximately
3.02 billion bases. For more statistics and details
on the assembly process, refer to the WUSTL
Callithrix_jacchus-2.0.2
assembly page.
Bulk downloads of the calJac1 sequence and annotations may
be obtained from the Genome Browser
FTP server or
Downloads
page. The sequence data can also be obtained directly from
WUSTL. See the WUSTL
data use policy for conditions of use.
Please acknowledge WUSTL School of Medicine Genome
Sequencing Center in any publications that result from the
use of this sequence assembly.
We'd like to thank WUSTL School of Medicine Genome
Sequencing Center for providing this assembly. The
initial set of marmoset browser annotation tracks were
generated by UCSC. The UCSC marmoset Genome Browser team is
Hiram Clawson, Robert Kuhn, Pauline Fujita, Brooke Rhead,
and Donna Karolchik. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
15 Apr. 2008 - Introducing the Archaeal Genome Browser Database
We'd like to introduce the Archaeal Genome Browser Database,
a visualization tool and an integrated repository for
archaeal functional genomics data. This resource was
developed by the
Lowe
Lab in the UCSC Biomolecular Engineering Department,
with key assistance from the UCSC Genome Browser team.
The Archaeal Genome Browser Database home page can be
accessed via the
Archaeal Genomes menu link on
the Genome Browser home page.
Currently there are more than 50 completed archaeal genomes,
the least studied domain of life. Although archaea and
bacteria are both prokaryotes, often co-existing in the
same environments, many aspects of archaeal cell biology
such as DNA replication, repair, transcription, and
translation are homologous to those found in eukaryotes.
Some members of archaea are also notable for inhabiting
extreme environments, including boiling terrestrial hot
springs, black smoker vents at the bottom of the ocean,
the ultra briny water of the Dead Sea, and highly acidic
drainage water from ore mines, to name a few.
The Archaeal Genome Browsers offer a variety of basic tracks
derived from Genbank RefSeq annotation, along with published
genome analyses from the Lowe Lab and external groups. The
annotations include operon predictions, regulatory sequence
motifs (promoters and Shine-Dalgarno), microarray data,
multi-genome alignments, and protein conservation across
major phylogenetic groups.
The goal of the Lowe Lab is to make the Archaeal Genome
Browser Database a forum for ongoing community-based genome
annotation, and they welcome new experimental and
bioinformatic analyses. If you would like to contribute
data, or have questions or feedback about the database,
contact
Todd Lowe.
8 Apr. 2008 - Updated Cow Genome Browser Now Available
The UCSC Genome Bioinformatics Group has released a Genome
Browser and Blat server for the Oct. 2007 draft assembly of
the Cow genome Bos taurus. This assembly
(UCSC version bosTau4) was produced by the Baylor College of
Medicine Human Genome Sequencing Center (BCM HGSC) as
Baylor release Btau_4.0.
The Btau_4.0 release was produced using the
Atlas
genome assembly system at BCM HGSC.
The sequencing strategy combined BAC shotgun reads with
whole genome shotgun reads from small insert libraries as
well as BAC end sequences. The assembly contains chromosomes
1-29 and X as well as 11869 scaffolds (named chrUn.004.*).
The mitochondrial sequence (available in the browser as
"chrM") was obtained from Genbank accession
GI:60101824.
The Btau_4.0 assembly was tested against available bovine
sequence data sets (EST sequences and finished BAC
sequences) for extent of coverage (completeness). When
assembled contigs were tested, over 95% of the sequences in
these data sets were found to be represented, indicating
that the shotgun libraries
used to sequence the genome were comprehensive. Of the 1.04
million EST sequences 95.0% were contained in the assembled
contigs. Assuming the ESTs are uniformly distributed
throughout the genome, the estimated genome size is
2.73Gb/95% = 2.87Gb.
For detailed information on the sequencing and assembly
techniques, see the Baylor
Bovine Genome Project web page.
For a list of the chromosomes and scaffolds in this
assembly, click the "Sequences" link on the cow
browser
gateway
page.
Bulk downloads of the sequence and annotation data are
available via the Genome Browser
FTP
server or
Downloads
page. These data have
specific conditions for use. The cow
annotation tracks were
generated by UCSC and collaborators worldwide.
We'd like to thank Baylor College of Medicine for providing
this assembly. The UCSC bosTau4 browser and documentation
were produced by Hiram Clawson, Brian Raney, and Ann Zweig.
See the Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
24 Mar. 2008 - Free Genome Browser Institutional Seminars
The UCSC Bioinformatics Group announces your chance to
bring our hands-on computer workshop on the UCSC Genome
Browser to your institution. The seminar is presented by
our training partner, OpenHelix.
The 3-1/2-hour introductory tutorial will cover the topics
needed to effectively use our tool set, including: basic
functionality of Genome Browser searching and BLAT use,
Table Browser use, creating and using Custom Tracks, and
an introduction to the Gene Sorter. The workshop material
requires knowledge of genomic/biological concepts, but no
programming skills are required.
Participants will receive slide hand-outs, exercises, and
UCSC Genome Browser and Table Browser Quick Reference Cards.
To bring the seminar to your institution, apply on the
OpenHelix website. Participating institutions are
required only to:
--Provide a computer classroom with internet access. The
preferred number of computers is 24 or above. As an
alternative to a computer room, the institution may provide
a classroom with wireless access and ask participants to
bring their own laptops. The seminar can be done in the
morning and repeated in the afternoon to reach more users.
--Conduct outreach and communication to participants as
necessary.
The number of seminars is limited -- apply today!
Contact information: www.openhelix.com or 1-888-861-5051.
About OpenHelix, LLC: OpenHelix provides the genomics
knowledge you need when you need it. OpenHelix offers
online self-run tutorials, web seminars, and on-site
training for institutions and companies on the most
powerful and popular free, web-based, publicly accessible
bioinformatics resources. In addition, OpenHelix is
contracted by resource providers to provide comprehensive,
long-term training and outreach programs. The company
has its headquarters in Seattle, with offices in San
Francisco and Boston. Further information can be found at
www.openhelix.com or by calling 1-888-861-5051.
10 Mar. 2008 - Orangutan Genome Browser Now Available
The UCSC Genome Bioinformatics Group has released a Genome
Browser and Blat server for the Jul. 2007 draft assembly of
the Sumatran orangutan genome, Pongo pygmaeus
abelii. This assembly (UCSC version
ponAbe2, WUSTL version Pongo_albelii-2.0.2) was provided by
the Genome Sequencing Center at Washington University School
of Medicine in St. Louis (WUSTL), MO, USA.
The orangutan genome was sequenced to 6X coverage
using a female orangutan known as "Susie" from
the Gladys Park Zoo (Brownsville, TX, USA). The combined
sequence reads were assembled using
PCAP and filtered for all
known non-orangutan sequence contaminants. For more details
about the assembly, see the orangutan browser
gateway
page and the WUSTL
Pongo abelii web page.
Of the 3.09 Gb of total sequence, 3.08 Gb are ordered and
oriented along the chromosomes. Gap sizes between
supercontigs were estimated based on their size in human,
with a maximum gap size of 30 kb allowed. For a list of the
chromosomes in this assembly, click the
"Sequences" link on the orangutan browser
gateway
page.
The mitochondrial sequence is also available as the virtual
chromosome "chrM".
Bulk downloads of the sequence and annotation data are
available via the Genome Browser
FTP
server or
Downloads
page. These data have
specific
conditions for use. The orangutan browser annotation
tracks were generated by UCSC and collaborators worldwide.
We'd like to thank WUSTL for providing this
assembly. The UCSC ponAbe2 browser and documentation were
produced by Hiram Clawson, Kayla Smith, Robert Kuhn, Ann
Zweig and Donna Karolchik.
See the Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
7 Mar. 2008 - New Reverse Functionality Released
The Genome Browser team is happy to announce new
functionality in the main genome browser track display. A
new configuration button, "Reverse," now allows users to
view the entire browser image flipped right-to-left.
This is especially useful when a user's gene of interest
aligns on the opposite strand from the reference assembly.
Those genes then appear in the 5' to 3' direction.
When the reverse function has been activated, all of the
track labels usually displayed on the left side of the track
(including the mini-button providing access to configuration
options) are displayed on the right side. This allows users
to see at a glance which direction is being displayed. All
navigation options operate as expected.
Thanks to Mark Diekhans, Ann Zweig, Robert Kuhn and the
rest of the engineering team for implementing this feature.
In addition to the openings listed in the 12 Dec. 2007
announcement (see below), the UCSC Genome Browser project is
accepting applications for Research Software Architect,
a position in the UC Project Scientist academic series.
For the job description, qualifications and application
information, please
see the Center for Biomolecular Science and Engineering
website. To ensure full consideration,
applications must be received by 22 Jan. 2008.
The UCSC Genome Browser project is currently accepting
applications for two positions on our development team:
Software Development Engineer (Programmer/Analyst 3) and
Biological Database Testing/User Support Technician
(Programmer/Analyst 1).
We are looking for talented self-motivated individuals who
would like to use their skills in computer science,
biology, and bioinformatics on a fast-paced project
featuring the work of top genomics scientists worldwide.
For a summary of the position details and qualifications,
see the entries for
Software Developer and
Biological Database Testing/User Support
Technician on the Center for Biomolecular Science and
Engineering (CBSE) website. For detailed job descriptions
and application information, go to the
UCSC Staff
Employment website, click the "Search
Postings" link on the sidebar, and type in job
#0701419 (Software Developer) or job #0701391 (Testing/User
Support Technician).
15 Oct. 2007 - Genome Browser for Zebrafish Zv7 Released
The latest zebrafish assembly -- Zv7 (UCSC version
danRer5, July 2007) -- is now available in the UCSC
Genome Browser. The Zv7 assembly was produced by
The Wellcome Trust Sanger Institute in collaboration with
the Max Planck Institute for Developmental Biology in
Tuebingen, Germany, and the Netherlands Institute for
Developmental Biology (Hubrecht Laboratory), Utrecht,
The Netherlands.
This assembly consists of 1,440,582,308 bp in 5,036
fragments. It includes sequence anchored to chromosomes
1-25 and chrM (mitochondrial), as well as 5010 unplaced
scaffolds. The assembly was produced by integrating
finished clone sequence from the physical map with whole
genome shotgun assembly sequence. The N50 size is
1,153,933, n = 277 (i.e. the length such that 50% of the
assembled genome lies in blocks of the N50 size or longer).
For more information about this assembly, see the Sanger
Institute web page for the
Danio rerio Sequencing Project
and the track description page for the Assembly track.
The danRer5 sequence and annotation data can be
downloaded from the UCSC Genome Browser
FTP server
or
downloads
page. Please review the
guidelines for using these data.
We'd like to thank the Wellcome Trust Sanger Institute,
the Max Planck Institute for Developmental Biology,
Hubrecht Laboratory and the other
institutions who contributed to the sequencing and
mapping effort of this release. Special thanks to the
Zebrafish Genome Initiative at Children's Hospital in
Boston for their collaboration on this release.
The UCSC zebrafish Genome Browser
was produced by Rachel Harte, Ann Zweig, and Donna
Karolchik. The
initial set of annotation tracks was generated by the
UCSC Genome Bioinformatics Group. See the
credits
page for a detailed list of the organizations and
individuals who contributed to the release of
this browser.
10 Oct. 2007 - New Browser for Purple Sea Urchin
The Sep. 2006 release of the purple sea urchin genome
(Strongylocentrotus purpuratus) is now available
in the UCSC Genome Browser. This assembly, UCSC version
strPur2, was produced by the Baylor College of Medicine
Human Genome Sequencing Center (BCM HGSC) and corresponds
to their Spur_2.1 assembly.
The Spur_2.1 release was assembled from BAC sequence reads
(approximately 2x coverage) and whole genome shotgun
reads (6x coverage), and utilizes BAC tiling path
information. The BCM HGSC Atlas-2.0 genome
assembly system was used to generate this assembly.
The total length of all contigs greater than 1kb is 804
Mbp. When the gaps between contigs in scaffolds are
included, the total span of the assembly is 907 Mbp. The
estimated size of the genome based on the assembly is 814
Mbp.
Compared to previous sea urchin releases, the Spur_2.1
assembly is more continuous and has fewer false
duplications; contaminations identified in the previous
Spur_2.0 assembly have been removed.
This draft assembly may contain errors; therefore, users
should exercise caution. Typical errors may include
misassemblies of repeat sequences,
collapses of repeat regions, and artificial duplications in
polymorphic regions. However, base accuracy in contigs is
usually very high with most errors near the ends of contigs.
Bulk downloads of the sequence and annotation data are
available via the Genome Browser
FTP server
or the Downloads
page. These data have
specific conditions for use. The initial
set of strPur2 annotation tracks was generated by UCSC.
See the Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
4 Oct. 2007 - ENCODE Genome Browser Released for hg18 Assembly
The UCSC ENCODE browser for the human genome assembly hg18
(NCBI Build 36) is now available. You can access the browser
directly at
http://genome.ucsc.edu/ENCODE/encode.hg18.html
or by clicking the ENCODE link in the sidebar menu on this
page, then clicking the Regions (hg18) link in the sidebar
menu on the ENCODE portal page.
The hg18 ENCODE browser includes 540 data tables in 59
browser tracks that were migrated from the hg17 browser.
The hg17 data coordinates were converted to hg18 coordinates
using the UCSC liftOver process.
To improve the accessibility of the data, related ENCODE
tracks have been gathered into new configuration groupings
("super-tracks") that can be displayed or hidden
using a single visiblity control. We have also reduced the
number of track groups and have modified some of the group
names for clarity. ENCODE tracks with whole-genome data
have been moved into the standard browser track groups.
For more information about the hg18 ENCODE data migration,
see the News section on the UCSC
ENCODE portal page and the UCSC
genomeWiki.
22 Aug. 2007 - New Mouse Browser Released
The latest mouse genome assembly from the Mouse Genome
Sequencing Consortium, NCBI Build 37.1, is now available in
the UCSC Genome Browser. This version (UCSC version mm9) is
considered to be essentially finished.
The Build 37.1 assembly includes approximately 2.6 Gb of
sequence on chromosomes 1-19, X, Y, M (mitochondrial DNA)
and Un (unmapped clone contigs).
In-depth information about this assembly will become
available on the
NCBI website.
On chromosome Y in this assembly, only the short arm has
reliable mapping data; therefore, most of the contigs on
the Y chromosome are unplaced.
The mm9 sequence and annotation data may be downloaded
from the Genome Browser
FTP
server or
Downloads
web page. The mm9 annotation tracks were generated by UCSC
and collaborators worldwide.
NOTE: To expedite the availability of the mm9 browser on our
website, the initial release does not contain the
comparative genomics annotations. These will be added to
our website as they become available. Also, note that
the UCSC mm9 database contains only the reference strain
C57BL/6J.
We'd like to thank Deanna Church and the Mouse Genome
Sequencing Consortium for this assembly. We'd also like to
acknowledge the work of the UCSC mm9 team: Hiram Clawson,
Archana Thakkapallayil, Robert Kuhn, and Donna Karolchik.
For a complete list
of the individuals and organizations who participated
in this assembly, see the
Credits
page.
22 Aug. 2007 - Latest Bovine Assembly Available
The UCSC Genome Bioinformatics Group has released a
Genome Browser and Blat server for the Aug. 2006 Btau_3.1
draft assembly of the cow genome. This assembly (UCSC
version bosTau3) was provided by Baylor
College of Medicine Human Genome Sequencing Center in
Houston, TX.
The Btau_3.1 release was produced by the Atlas genome
assembly system at Baylor College of Medicine Human Genome
Sequencing Center. The sequencing strategy combined BAC
shotgun reads with whole genome shotgun reads from small
insert libraries as well as BAC end sequences. The assembly
contains chromosomes 1-29 and X as well as 13045 scaffolds
(named chrUn.003.*).
More information on the Btau_3.1 assembly can be found on
the Baylor
Bovine Genome Project web page and the
Readme file that accompanies this release.
Bulk downloads of the sequence and annotation data are
available via the Genome Browser
FTP server or
Downloads
page. Please refer to the Baylor
conditions of use regarding these
data. The bosTau3 annotation tracks were generated by
UCSC and collaborators worldwide.
We'd like to thank Baylor College of Medicine for
the bovine sequence and assembly. We'd also like to
acknowledge the members of the UCSC Genome Bioinformatics
Group who contributed to the Cow Genome Browser:
Heather Trumbower, Angie Hinrichs, Kayla Smith, and Donna
Karolchik. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
2 Aug. 2007 - Five New Worm Assemblies
We've updated our existing nematode browsers--for C.
elegans and C. briggsae--to the latest
publicly available assemblies. In addition, we've added
three new worms to our collection: C. brenneri
(Caenorhabditis n. sp. PB2801), C. remanei,
and Pristionchus pacificus. The C. elegans
sequence was obtained from WormBase; the Genome Sequencing
Center at Washington University in St. Louis (WUSTL)
provided sequence data for the other four assemblies.
SPECIES
UCSC VERSION
RELEASE DATE
SOURCE/RELEASE
C. elegans
ce4
Jan. 2007
WormBase v. WS170
C. briggsae
cb3
Jan. 2007
WUSTL Cb3
C. brenneri
caePb1
Jan. 2007
WUSTL 4.0
C. remanei
caeRem2
Mar. 2007
WUSTL 1.0
P. pacificus
priPac1
Feb. 2007
WUSTL 5.0
Bulk downloads of the sequence and annotation data are
available via the Genome Browser
FTP
server or
Downloads
page. Please review the
data use policy for the WUSTL-generated
assemblies.
We'd like to thank WUSTL, WormBase, and the Sanger Institute
for providing the sequence data for these assemblies.
The UCSC worm browsers were produced by Hiram Clawson,
Kayla Smith, Brooke Rhead, Ann Zweig, and Donna Karolchik.
See the Genome Browser
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
13 Jul. 2007 - Drosophila melanogaster Release 5 Now Available in Genome Browser
The latest D. melanogaster assembly can now
be viewed in the UCSC Genome Browser. This version --
Release 5, dated Apr. 2006 (UCSC version dm3) -- was
provided by the Berkeley Drosophila Genome Project (BDGP)
and combines both
euchromatic and heterochromatic sequence. The Release 5.1
annotations (Mar. 2007) were provided by
FlyBase.
The six euchromatic arms in this assembly were sequenced and
assembled by BDGP from a combination of BAC and whole genome
shotgun data, and have been finished to high quality. All
euchromatic sequence have been compared to the restriction
digest fingerprints in multiple enzymes for validity. The
details of this analysis will be described in a forthcoming
publication.
Heterochromatic sequence from the
Drosophila
Heterochromatin Genome Project (DHGP) are also available in this assembly. Scaffolds that could not be unambiguously
mapped to a chromosome arm have been concatenated into
chrUn. chrUextra contains small scaffolds produced by the
Celera shotgun assembler that could not be consistently
joined with larger scaffolds. Because some of the
chrUextra data are of low quality, researchers are
encouraged to contact either BDGP or DHGP for further
details on this resource. For more information on this
assembly, see the Release 5
assembly release notes.
Bulk downloads of the sequence and annotation data are
available via the Genome Browser
FTP
server or
Downloads
page.
We'd like to thank the BDGP, DHGP, and Flybase for
providing data for this release. The dm3 Genome Browser
was produced by Angie Hinrichs, Archana Thakkapallayil,
Kayla Smith, and Donna Karolchik.
The D. melanogaster browser annotations were
generated by FlyBase, DHGP, and the UCSC Genome
Bioinformatics group. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
26 Jun. 2007 - New 28-Species Conservation Track Released
We are pleased to announce the release of new versions of
the Conservation and Most Conserved annotation tracks for
the Human March 2006 Genome Browser (hg18, NCBI Build 36).
The new Conservation track displays multiple alignments of
27 vertebrate species aligned to the human genome, along
with measurements of evolutionary conservation across all
species in the alignment and a separate measurement of
conservation across the placental mammal subset of species
in the alignment.
The new track includes:
5 new high-quality assemblies -- horse, platypus,
lizard, and two fish (stickleback and medaka)
6 new low-coverage mammalian genomes -- bushbaby,
tree shrew, guinea pig, hedgehog, common shrew, and cat
10 assemblies included in the previous version of the
track -- rhesus, mouse, rat, rabbit, dog, armadillo,
elephant, tenrec, opossum, and tetraodon
UCSC hosts browsers for the high-quality assemblies and
the cat. Masked sequence data for the other genomes in the
track are available from our downloads server.
In addition to the expanded species list, the new
Conservation track features the following improvements:
additional filtering of pairwise alignments for each
species to reduce paralogous alignments
information about the quality of aligning species sequence
included in the multiple alignment downloads
new track configuration buttons to assist in selecting
which species to display
The previous 17-vertebrate versions of the Conservation and
Most Conserved tracks remain available on the hg18 Genome
Browser as the "17-Way Cons" and "17-Way Most
Cons" tracks.
13 Jun. 2007 - ENCODE Findings Released to Public
The findings of the ENCODE project have been
released to the public today, the culmination of a
four-year effort to catalog the biologically functional
elements in 1 percent of the human genome. The publications,
which include a group paper in the 14 June 2007 issue of
Nature and 28 companion papers in
the June 2007 issue of
Genome Research, were authored by
researchers from academic, governmental, and industry
organizations located in 11 countries. The Nature
issue includes a pull-out poster featuring a screenshot of
the UCSC Genome Browser displaying a broad range of the
ENCODE data.
In the press release accompanying the publication
rollout, NHGRI Director Francis S. Collins is quoted as
saying
"This impressive effort has uncovered many exciting
surprises and blazed the way for future efforts to explore
the functional landscape of the entire human genome. Because
of the hard work and keen insights of the ENCODE consortium,
the scientific community will need to rethink some long-held
views about what genes are and what they do, as well as how
the genome's functional elements have evolved. This could
have significant implications for efforts to identify the
DNA sequences involved in many human diseases."
The main portal for the ENCODE data is the UCSC ENCODE
Genome Browser. The analysis effort has been coordinated
by Ensembl. Much of the primary data have
been deposited in the
NCBI GEO and
EBI ArrayExpress databases.
To access the UCSC Genome Browser ENCODE portal, click the
ENCODE link in the left sidebar menu
on the Genome Browser home page.
For more information on the ENCODE project,
including the consortium's data release and accessibility
policies and a list of NHGRI-funded participants, see the
NHGRI ENCODE website. To read more about
UCSC's role on the project, see the
news release on the UCSC Center for
Biomolecular Science and Engineering website.
25 May 2007 - Platypus Assembly Available
We have released a Genome Browser and Blat server for
the Jan. 2007 v5.0.1 draft assembly of Ornithorhynchus
anatinus (UCSC version ornAna1) produced by the
Genome Sequencing Center at Washington
University, St. Louis, MO (WUSTL).
This assembly, which was sequenced using a combination of
whole genome shotgun plasmid, fosmid and BAC end sequences,
has a coverage of approximately 6X. It is comprised of
about 1.84 Gb of actual sequence (excluding gap estimates),
with 437 Mb anchored and ordered on chromosomes.
We'd like to thank WUSTL for providing this assembly. The
platypus Genome Browser was produced by Angie Hinrichs,
Kayla Smith, Robert Kuhn, Brian Raney, and Donna Karolchik.
The platypus browser annotation tracks were generated by
UCSC and collaborators worldwide. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
17 May 2007 - Lizard Assembly Available in Genome Browser
A Genome Browser and Blat server are now available for
the Feb 2007 v1.0 draft assembly (UCSC version anoCar1) of
Anolis carolinensis produced by the
Broad
Institute.
This assembly has been sequenced to 6.8X coverage. The draft
sequence contains 7,233 scaffolds comprised of nearly 1.74
Gb.
We'd like to thank the Broad Institute for providing this
assembly. The lizard Genome Browser was produced by Hiram
Clawson, Archana Thakkapallayil, Robert Kuhn, and Donna
Karolchik. The lizard browser annotation tracks were
generated by UCSC and collaborators worldwide. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
16 May 2007 - New Dates for OpenHelix Seminars in L.A., D.C., Phila.
The dates for the upcoming OpenHelix Genome Browser seminars
in Washington, D.C. and Los Angeles, CA have been changed.
The following updated announcement includes the new dates:
The UCSC Bioinformatics Group announces three regional
seminars and hands-on computer workshops on the UCSC
Genome Browser presented by
OpenHelix:
Philadelphia -- Wednesday, 13 June
Washington. D.C./Baltimore -- Wednesday, 20 June
Los Angeles -- Wednesday, 27 June
All sessions will be held 1 p.m. to 4 p.m.
These introductory sessions are geared towards anyone with a
basic knowledge of genomic and biological concepts who is
interested in learning how to use the UCSC Genome Browser.
No programming experience is required. The seminars will
cover the topics necessary to learn how to effectively use
the browser tool set, including basic Genome Browser
functionality, searching and BLAT use, Table Browser use,
creating and using custom annotation tracks, and an
introduction to the Gene Sorter. Lectures will be
accompanied by hands-on computer exercises conducted
directly on the Genome Browser web site. Participants
receive a complete set of slide and exercise handouts and
printed Quick Reference Cards.
For further information or to make a reservation, visit the
OpenHelix website or call 1-888-861-5051.
Register early; seating is limited. Academic and student
discounts are available.
14 May 2007 - Horse Genome Browser Now Available
The Jan. 2007 EquCab1 release of the horse genome
(Equus caballus) is now available
in the UCSC Genome Browser. This assembly, UCSC version
equCab1, was produced by the
Broad
Institute.
The horse draft genome has been sequenced to 6.8X coverage.
Approximately 84% of the sequence has been anchored to
chromosomes, which include autosomes 1-31 and sex
chromosome X. Unanchored contigs that could not be
localized to a chromosome have been concatenated into the
virtual chromosome "chrUn", separated by gaps of
1,000 bp. The mitochondrial sequence is also available in
the Genome Browser as the virtual chromosome
"chrM". For more details about the assembly, see
the Broad Institute
Horse Genome Project page.
The UCSC Horse Genome Browser was produced by Fan Hsu,
Brooke Rhead, Robert Kuhn, Hiram Clawson, Angie Hinrichs,
Kate Rosenbloom, and Donna Karolchik. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
27 April 2007 - Medaka Genome Browser Released
We're happy to announce the release of a Genome Browser and
Blat server for the Medaka Version 1.0 draft assembly (Apr.
2006, UCSC version oryLat1). This assembly was produced in
Japan by the National Institute of Genetics (NIG) and
the University of Tokyo. It is
equivalent to Ensembl's Oct. 2005 MEDAKA1 data set.
The v1.0 assembly has been sequenced to 10.6X coverage. It
consists of approximately 700.4 million bp (excluding gaps)
on chromosomes 1-24. 7,299 scaffolds comprised of
nearly 36,500
contigs of unplaced sequence are displayed on the
virtual chromosome "chrUn". These contigs are spaced with a
10 bp gap; scaffold gaps are 100 bp in size. The medaka
mitochondrial sequence is also available in the Genome
Browser as the virtual chromosome "chrM".
Bulk downloads of the sequence and annotation data are
available via the Genome Browser
FTP
server or the Downloads
page. See the University of Tokyo medaka website for the
data release policy for this assembly.
The Medaka browser annotation tracks were generated by
UCSC and collaborators worldwide. See the Genome Browser
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
18 April 2007 - Free Genome Browser Seminar at Experimental Biology 2007
OpenHelix will present a free introductory seminar on the
Genome Browser during Experimental Biology 2007,
April 29-May 1, in Washington, D.C. The tutorial will cover
the topics needed to effectively use the Genome Browser,
including: basic functionality
of Genome Browser searching and BLAT use, Table Browser use,
creating and using Custom Tracks, and an introduction to the
Gene Sorter.
The seminar will be held on Monday April 30, 4:30-5:30p.m.
in Room 204C in the Washington, D.C. Convention Center. It
is open to any interested conference attendee with a basic
knowledge of genomic/biological concepts; no programming
skills are needed.
The tutorial requires no advanced registration or fee.
Attendees will receive a free download of the training
materials. For more information, see the
OpenHelix
website or call 1-888-861-5051.
In addition to the tutorial, OpenHelix will be presenting
brief introductory overviews of the UCSC Genome Browser and
other bioinformatics resources during show hours at Booth
330/332. Stop by the booth for more information and to
receive your free Genome Browser Quick Reference Cards.
11 April 2007 - Latest Fugu Assembly Available in Genome Browser
The UCSC Genome Browser now includes the latest
release of the Fugu genome. The v4.0 whole genome shotgun
assembly (Oct. 2004, UCSC fr2) was provided by the
US DOE Joint Genome Institute (JGI) as part of the
International Fugu Genome Consortium led by the JGI and the
Singapore Institute of Molecular and Cell Biology (IMCB).
This version has been sequenced to approximately 8.5X
coverage. The assembly contains 7,213 scaffolds covering
393,312,790 bp. The UCSC browser displays the scaffolds on
the virtual chromosome chrUn with gaps of 1,000 bp
between scaffolds. The scaffolds range in size from 2,223 bp
to 7,245,445 bp. Fifty percent of the sequence (196,648,171
bp) is contained within 125 scaffolds of size 858,115 or
greater (N50). The Fugu mitochondrial sequence is also
available as the virtual chromosome chrM
(GenBank accession: NC_004299.1).
Bulk downloads of the sequence and annotation data are
available via the Genome Browser
FTP server or
Downloads page. These data have been
freely provided by the JGI for use in the UCSC Genome
Browser.
Many thanks to the JGI, IMCB, and the International Fugu
Genome Consortium for the assembly data.
The UCSC Fugu Genome Browser was produced by Cory McClean,
Hiram Clawson, Ann Zweig, and Donna Karolchik.
The annotation tracks were generated by UCSC
and collaborators worldwide. See the
Credits page for a detailed list of the
organizations and individuals who
contributed to this release.
6 April 2007 - New UCSC Gene Prediction Set Released
We are pleased to announce the release of a new gene
prediction set, UCSC Genes, on the latest human
Genome Browser (hg18, NCBI Build 36). This annotation,
which includes putative non-coding genes as well as
protein-coding genes and 99.9% of RefSeq genes,
is the next generation of the Known Genes set that UCSC
has been providing for several years and supersedes the
existing Known Genes annotation on the hg18 assembly.
The UCSC Genes is a moderately conservative prediction set
based on data from RefSeq, GenBank, and UniProt. Each
entry requires the support of one GenBank RNA sequence plus
at least one additional line of evidence, with the exception
of RefSeq RNAs, which require no additional evidence.
Some of the non-coding transcripts in the set may actually
code for protein, but the evidence for the associated
protein is weak at best. Compared to RefSeq, this gene set
generally has about 10% more protein-coding genes,
approximately five times as many putative non-coding genes,
and about twice as many splice variants.
A new companion track to UCSC Genes, Alt Events, shows
various types of alternative splicing, alternative promoter,
and other events that result in more than a single
transcript from the same gene. This track is based on an
analysis by the txgAnalyse program of splicing graphs
produced by the txGraph program.
The UCSC Genes set is produced using a computational
pipeline developed at UCSC by Jim Kent, Chuck Sugnet and
Mark Diekhans. The programs used to construct the Alt Events
data set were written by Jim Kent. For detailed information
about the process used to construct the genes set, see the
track
description page. In upcoming months, we plan to
release UCSC Genes sets on several organisms in addition
to human. The UCSC Genes annotations will be updated
approximately every three months.
As part of this change, we are now using our own UCSC
Genes accession numbers as the primary key into the
underlying knownGene table, rather than the GenBank mRNA
accessions
we used in the previous Known Genes prediction set.
Note that this may affect external sites with URLs that
link into our genes track using the older-style accessions.
We will continue to provide the older Known Genes track on
hg18 under the name "Old Known Genes". You may
find the following tables useful in referencing the older
gene set and converting between the two sets:
knownGeneOld2: new name for table underlying the old Known
Genes (previously called knownGene)
kgXrefOld2: new name for table that contains data for
converting old Known Genes IDs to other IDs (previously
called kgXref)
kg2ToKg3: data for converting old Known Genes IDs
to the newer UCSC Genes IDs
We'd like to acknowledge the many people affiliated with
the UCSC Genome
Bioinformatics group who worked hard to release this new
annotation: developers Jim Kent,
Mark Diekhans, and Fan Hsu (with technical support from
several
other engineers in the group); David Haussler; our splendid
QA team --
Archana Thakkapallayil, Ann Zweig, Robert Kuhn, Kayla Smith,
and Brooke Rhead; our build engineer -- Andy
Pohl; and our sysadmin group. We'd also like to thank Chuck
Sugnet for his input, the people and organizations
maintaining the RefSeq, UniProt, and GenBank databases, and
the scientists worldwide who have contributed to them. If
you have any questions about this new release,
feel free to contact us at
genome@soe.ucsc.edu
(general questions) or
genome-mirror@soe.ucsc.edu
(mirror-specific questions).
27 March 2007 - Stickleback Assembly Released in Genome Browser
We have released a Genome Browser and Blat server for
the Feb. 2006 v1.0 draft assembly of Gasterosteus
aculeatus produced by the
Broad
Institute.
This assembly has been sequenced to approximately 6X
coverage. An estimated 87% of the sequence has been
anchored to chromosomes (chrI - chrXXI). Of the remaining
unanchored scaffolds, those that could be localized to a
chromosome have been concatenated into the virtual
chromosome "chrUn" with 1000bp gaps between
scaffolds. The stickleback mitochondrial sequence is also
available as the virtual chromosome "chrM".
The stickleback browser annotation tracks were generated by
UCSC and collaborators worldwide. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
16 February 2007 - New Browser Session-Sharing Function Available
We are pleased to announce the release of a new session
management functionality
in the Genome Browser, which allows users to save and
share browser sessions.
Users are now able to configure their browsers with specific
track combinations, including custom tracks, and
save the configuraton options. Multiple sessions may
be saved for future reference, for comparison of scenarios
or for sharing with colleagues. Saved sessions persist for
one year after the last access, unless deleted. Custom tracks
persist for at least 48 hours after
the last time they are viewed.
The new feature may be accessed via the "Sessions" link
in the top blue bar in any assembly. To ensure privacy
and security, users must login to the genomewiki site
and create a username and password. Individual sessions
may be designated by the user as either "shared" or
"non-shared" to protect the privacy of confidential data.
To avoid having a new shared session from someone else
override existing Genome Browser settings,
users are encouraged to open a new web-browser instance
or to save existing settings in a session before loading
a new shared session.
The Sessions feature was written by Angie Hinrichs of the
UCSC Genome Bioinformatics Group and released with the
assistance of Kayla Smith and Robert Kuhn.
2 February 2007 - New Genome Graphs Tool Available
in Genome Browser
We are pleased to announce the release of a new software
tool in the Genome Browser collection, the
Genome Graphs
tool. Genome Graphs offers the ability to
upload and display genome-wide data sets such as the
results of genome-wide SNP association studies, linkage
studies and homozygosity mapping. The Genome Graphs tool
may be accessed from the menu on the UCSC Genome
Bioinformatics home page.
The initial release of Genome Graphs includes the
following features:
upload several sets of genome-wide data and display
them simultaneously
click on an area of interest and go directly to the
genome browser at that position
set a significance threshold for your data and view
only regions that meet that threshold
view the genes that exist in areas where your data
meet your significance threshold
For more information about the Genome Graphs tool, visit
the Gateway page or consult the
Getting
Started on Genome Graphs
section in the User's Guide.
Genome Graphs was written by Jim Kent of the UCSC Genome
Bioinformatics Group and released with the assistance of
Ann Zweig.
22 January 2007 - Cat Assembly Available in Genome Browser
The Mar. 2006 release of Felis catus (UCSC version
felCat3) is now available in the Genome Browser. This
assembly was produced by The Broad Institute of MIT/Harvard and
Agencourt Bioscience.
The felCat3 genome has been sequenced to 2X coverage and
consists of 217,790 scaffolds. The total contig length for
this assembly is approximately 1.6 Gb spanning nearly 4.0
Gb (with 60.1% in gaps). There are 749,376 contigs, with an
N50 length of 2,506 bases. There are 149,283 supercontigs,
with an N50 length of 49,769 bases (not including gaps).
The N50 size is the length such that 50% of the assembled
genome lies in blocks of the N50 size or longer.
The felCat3 sequence and annotation data can be downloaded
from the Genome Browser
FTP server or Downloads
page. Please review the
guidelines
for using the cat assembly data.
Many thanks to The Broad Institute for providing these data.
The UCSC cat Genome Browser was produced by Heather Trumbower,
Angie Hinrichs, Mark Diekhans, Brooke Rhead, and Archana
Thakkapallayil. The
initial set of annotation tracks was generated by the UCSC
Genome Bioinformatics Group. See the Genome Browser
Credits
page for a
detailed list of the organizations and individuals who
contributed to the release of this browser.
The UCSC Bioinformatics Group announces four regional
seminars and hands-on computer workshops on the UCSC
Genome Browser, presented by
OpenHelix:
San Francisco, CA -- Wednesday, 31 January
Seattle, WA -- Thursday, 1 February
New York City, NY -- Tuesday, 13 February
Cleveland, OH -- Wednesday, 14 February
Two sessions will be offered for the New York and Cleveland
seminars: 9:00 a.m. to noon and 1 p.m. to 4 p.m. Only the
afternoon session will be offered in San Francisco and
Seattle.
These introductory sessions are geared towards anyone with a
basic knowledge of genomic and biological concepts who is
interested in learning how to use the UCSC Genome Browser.
No programming experience is required. The seminars will
cover the topics necessary to learn how to effectively use
the browser tool set, including basic Genome Browser
functionality, searching and BLAT use, Table Browser use,
creating and using custom annotation tracks, and an
introduction to the Gene Sorter. Lectures will be
accompanied by hands-on computer exercises conducted directly
on the Genome Browser web site. Participants receive a
complete set of slide and exercise handouts and printed
Quick Reference Cards.
For further information or to make a reservation, visit the
OpenHelix website or call 1-888-861-5051.
Register early; seating is limited. Academic and student
discounts are available.
13 November 2006 - UCSC Genome Browser Wiki
The UCSC Genome Bioinformatics group has launched a wiki
site for sharing information about the UCSC Genome Browser
and its data. The wiki -- at
http://genomewiki.ucsc.edu
-- provides an informal forum for our browser users, mirror
sites, and staff to discuss topics of interest in the
genome biology field and exchange usage tips,
scripts/programs, and notes about mirroring the Genome
Browser and working with the Genome Browser source.
As with most wiki pages, general users are welcome to edit
and add pages (login required). Please note that all content
created on the genomewiki site becomes a public resource;
content persists in the history of a page even after it has
been deleted.
24 October 2006 - Free Genome Browser Training Sessions at AHA Scientific Sessions
OpenHelix will present a free seminar on
the UCSC Genome Browser at the American Heart Association's
Scientific Sessions 2006 in Chicago, IL, on 12 Nov. from
7:00 - 8:30 p.m. The seminar will be held in the Hyatt
Regency Conference Center, Room CC21, 2233 South Martin
Luther King Drive, Chicago, IL.
The introductory tutorial will cover the topics needed to
effectively use the Genome Browser including: basic
functionality of Genome Browser searching and BLAT use,
Table Browser use, creating and using Custom Tracks, and an
introduction to the Gene Sorter. The jointly-sponsored
seminar will also include an introduction to VISTA
comparative genomics tools.
The session is open to anyone attending the AHA Scientific
Sessions; no registration or fee is required. Participants
should have a basic knowledge of
genomic/biological concepts, but no programming skills
are needed. Attendees will receive a free
download of training materials, and refreshments will be
served. This event is not part of the official Scientific
Sessions 2006 as planned by the AHA Committee on Scientific
Sessions Program.
OpenHelix will also be presenting brief introductory
overviews of the Genome Browser and other resources during
show hours at booth 2464. Stop by the booth for more
information and to receive your free Quick Reference Cards
for the Genome Browser and Table Browser.
6 October 2006 - Announcing Upgrades to the Genome Browser Custom Tracks Functionality
We have enhanced one of the popular tools in the Genome
Browser collection: the custom
tracks utility.
The new custom tracks tool provides a more user-friendly
interface and increased flexibility for creating and
managing your custom tracks.
The initial release of this upgraded tool includes the
following features:
Add and display multiple custom tracks simultaneously
via URL, file or text
Add to, delete and modify the uploaded custom tracks
set using a new track management interface
Load and manage custom tracks from multiple assemblies
Create and upload description pages for custom tracks
Custom tracks will now persist on our server for
48 hours after last access (rather than 8 hours)
For more information about the new custom tracks
functionality, see the Genome Browser
Users's Guide.
The hgCustom CGI was written by Kate Rosenbloom with the
assistance of Archana Thakkapallayil, Ann Zweig and other
members of the UCSC Genome Bioinformatics Group.
7 September 2006 - Old Rhesus Assembly Archived
The Jan. 2005 rheMac1 draft assembly has been archived.
The data remain available on our
downloads
server, but blat services are no longer supported.
8 August 2006 - New Opossum Assembly Available in Genome Browser
The UCSC Genome Browser now includes the latest draft
assembly of the opossum genome. The Jan. 2006 release of
Monodelphis domestica (UCSC version monDom4) was
sequenced and assembled by
The Broad Institute, Cambridge, MA, USA.
This draft, which has approximately 6.5X coverage, has an
assembly length of nearly 3.61 billion bp including gaps
(3.50 billion bp without gaps) contained on chromosomes 1-8,
X, and Un. The N50 of the genome
including gaps is 104,359 bp; the N50 without gaps is
107,990. The N50 size is the length such that 50% of the
assembled genome lies in blocks of the N50 size or longer.
The monDom4 sequence and annotation data can be downloaded
from the Genome Browser
FTP server or
Downloads
page. Please review the
guidelines
for using the opposum assembly data.
Many thanks to The Broad Institute for providing these data.
The UCSC opossum Genome Browser was produced by Hiram
Clawson, Archana Thakkapallayil, Ann Zweig, Kayla Smith and
Donna Karolchik. The
initial set of annotation tracks was generated by the UCSC
Genome Bioinformatics Group. See the Genome Browser
Credits
page for a
detailed list of the organizations and individuals who
contributed to the release of this browser.
1 August 2006 - v2.1 Chicken Assembly Available in Genome Browser
We have updated the Chicken Genome Browser to include the
May 2006 v2.1 assembly (UCSC version galGal3) produced by
the Genome Sequencing Center at the Washington University
School of Medicine in St. Louis, MO, USA (WUSTL). The
source of this sequence was a female inbred Red Jungle Fowl
(Gallus gallus), the ancestor of domestic chickens.
The chicken genome is the first of the avian genomes to be
sequenced.
In this assembly, 198,000 additional reads covering all
contig ends and regions of low quality have been added to
the original assembly's 6.6X coverage. Approximately 95% of
the sequence has been anchored to chromosomes, which include
autosomes 1-24, 26-28, and 32, and sex chromosomes W and Z.
(In contrast to mammals, the female chicken is heterogametic
(ZW) and the male is homogametic (ZZ).) The remaining
unanchored contigs that could be localized to a chromosome
have been concatenated into the virtual chromosomes
"chr*_random", separated by gaps of 10,000 bp.
Unanchored contigs that could not be localized to a
chromosome have been concatenated into the virtual
chromosome "chrUn_random", separated by gaps of
100 bp to reduce the total size of chrUn_random. The chicken
mitochondrial sequence is also available as the virtual
chromosome "chrM".
Although centromere positions are indicated on this
assembly, little is known of their exact sequence.
The centromeres of 18 chromosomes were tentatively localized
based on FISH hybridization using BAC clones, genetic
markers flanking the centromeres in coordination with
mapping gaps in the physical map, repetitive sequence
content, and analysis of proximity to the constrictions of
the mitotic metaphase chromosomes. For more information on
the process used to create the chromosomal sequences and
assign centromere locations, see the WUSTL
Gallus gallus genome page.
We'd like to thank WUSTL, who provided the sequence,
physical map, assembly, and assembly/map for this
release. The genetic mapping and linkage analysis were
produced through a collaborative effort of labs in The
Chicken Mapping Consortium. The chicken browser annotation
tracks were generated by UCSC and collaborators worldwide.
See the
Credits
page for a detailed list of acknowledgements. The UCSC
Chicken Genome Browser was produced by Angie Hinrichs,
Kayla Smith, and Donna Karolchik.
20 July 2006 - New Chimpanzee Genome Browser Released
We are happy to announce the release of a Genome Browser for
the latest release of the chimpanzee (Pan troglodytes)
genome. The Mar. 2006 assembly -- labeled Chimp Build 2
Version 1 (UCSC version panTro2) -- was produced by the
Chimpanzee Sequencing and Analysis
Consortium.
The whole genome shotgun data were derived primarily from
the donor Clint, a captive-born male chimpanzee from the
Yerkes Primate Research Center in Atlanta, GA, USA. The
reads were assembled using the whole-genome assembly
program PCAP. For information about the assembly process,
see the panTro2
Gateway page.
This assembly covers about 97 percent of the genome and is
based on 6X sequence coverage. It is composed of 265,882
contigs with an N50 length of 29 kb and 44,460 supercontigs
with an N50 length of 9.7 Mb. The total contig length, not
including estimated gap sizes, is 2.97 Gb. Of that total,
2.82 Gb of sequence have been ordered and oriented along
specific chimpanzee chromosomes, 107 Mb have been placed in
chr*_random, and 50 Mb remain in chrUn.
A major difference between this assembly and the previous
Nov. 2003 version is the chromosomal numbering scheme,
which has been changed to reflect a new standard that
preserves orthology with human chromomes. Proposed by
E.H. McConkey in 2004, the new numbering
convention was subsequently endorsed by the International
Chimpanzee Sequencing and Analysis Consortium. This
standard assigns the
identifiers "2a" and "2b" to the
two chimp chromosomes that fused in the human genome to form
chromosome 2. Note that the genome assembly shown in the
Nov. 2003 panTro1 Genome Browser retains the older
numbering scheme, in which these chromosomes are numbered
12 and 13.
We'd like to thank the International Chimpanzee
Sequencing and Analysis Consortium, Washington
University at St. Louis School of Medicine Genome Sequencing
Center, and the Broad Institute for providing this sequence.
We'd also like to acknowledge the UCSC team who worked on
this release: Kate Rosenbloom, Brian Raney, Hiram Clawson,
Ann Zweig, Archana Thakkapallayil, and Donna Karolchik.
The chimpanzee browser annotation tracks were generated by
UCSC and collaborators worldwide.
20 June 2006 - Genome Browser Released for Baylor v3.4 Rat Assembly
The UCSC Genome Bioinformatics group has released a Genome
Browser for the v3.4 rat (Rattus
norvegicus) genome. This assembly--UCSC version rn4,
November 2004--was produced by the Atlas group at
Baylor
Human Genome Sequencing Center (HGSC) as part of the
Rat Genome Sequencing Consortium.
The sequence was assembled using a hybrid approach that
combines the clone-by-clone and whole genome shotgun
methods. The assembly is a minor update to version 3.3 that
spliced in 54.6 Mb finished BAC sequences; the overall
statistics are unchanged from releases 3.0 to 3.4.
The 3.x assemblies reflect several sequence additions and
software improvements over the previous 2.x assemblies,
including the sequencing of over 1100 new BACs to cover
gaps, an improved marker set from the Medical College of
Wisconsin, a new FPC map from the BC Cancer Agency Genome
Sciences Centre, and improved linking of bactigs. For
detailed information and statistics about the 3.x
assemblies, see the Baylor HGSC
Rat Genome Project web page.
Bulk downloads of the sequence and annotation data are
available via the Genome Browser
FTP
server or the
Downloads
page. These data are made available with
specific
conditions for use.
We'd like to thank the Rat Genome Sequencing Consortium
and the Baylor HGSC for providing this assembly. We'd also
like to acknowledge the UCSC team who produced the rn4
Genome Browser: Angie Hinrichs, Fan Hsu, Brooke Rhead,
Archana Thakkapallayil, Kayla Smith, Ann Zweig, Robert Kuhn,
and Donna Karolchik. The rn4 annotation tracks were
generated by UCSC and collaborators worldwide. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
12 June 2006 - Latest X. tropicalis Assembly Available in Browser
The v.4.1 Xenopus tropicalis assembly is now
available on the UCSC Genome Browser. This whole genome
shotgun assembly
(xenTro2, August 2005) was generated by the U.S. DOE
Joint Genome Institute (JGI) using the Jazz assembler.
It contains 19,501 scaffolds with an average coverage of
7.65X. Roughly half the genome is contained in 272
scaffolds, each of at least 1.56 Mb in length.
In this release, some scaffolds showing homology to a known
prokaryotic contaminant as well as non-cellular or vector
contamination have been removed by the JGI and placed in a
separate directory. The X. tropicalis assembly
will be improved over the coming year by additional
sequencing of large insert clones, targeted gap closure,
and the incorporation of physical and genetic mapping
information as it becomes available.
Many thanks to the JGI and the other
institutions who contributed to the sequencing and mapping
effort for this release. The xenTro2 Genome Browser was
produced by Angie Hinrichs, Kayla Smith, Robert Kuhn, and
Donna Karolchik. The xenTro2 annotation tracks were
generated by UCSC and collaborators worldwide. See the
credits page
for a detailed list of the organizations and individuals who
contributed to this release.
25 May 2006 - Zv6 Zebrafish Browser Released
The latest zebrafish assembly -- Zv6 (UCSC version
danRer4, March 2006) -- is now available in the UCSC
Genome Browser. The Zv6 assembly was produced by
The Wellcome Trust Sanger Institute in collaboration with
the Max Planck Institute for Developmental Biology in
Tuebingen, Germany, and the Netherlands Institute for
Developmental Biology (Hubrecht Laboratory), Utrecht,
The Netherlands.
This assembly consists of 1,626,077,335 bp in 6.653
scaffolds (N50 = 1,247,221 bp) with a sequence coverage of
approximately 6.5-7x. The sequence has been anchored to
chromosomes 1-25, chrM (mitochondrial), chrNA_random, and
chrUn_random.
For more information about this assembly, see the Sanger
Institute web page for the
Danio rerio Sequencing Project.
The danRer4 sequence and annotation data can be
downloaded from the UCSC Genome Browser
FTP server
or
downloads
page. Please review the
guidelines for using these data.
We'd like to thank the Wellcome Trust Sanger Institute,
the Max Planck Institute for Developmental Biology,
Hubrecht Laboratory and the other
institutions who contributed to the sequencing and
mapping effort of this release. Special thanks to the
Zebrafish Genome Initiative at Children's Hospital in
Boston for their collaboration on this release.
The UCSC zebrafish Genome Browser
was produced by Rachel Harte, Archana Thakkapallayil,
Robert Kuhn, Ann Zweig, and Donna Karolchik. The
initial set of annotation tracks was generated by the
UCSC Genome Bioinformatics Group. See the
credits
page for a detailed list of the organizations and
individuals who contributed to the release of
this browser.
10 May 2006 - NCBI Mouse Build 36 Released in Genome Browser
The latest mouse genome assembly from the Mouse Genome
Sequencing Consortium, NCBI Build 36, is now available in
the UCSC Genome Browser. This version (UCSC version mm8) is
considered to be essentially finished.
The Build 36 assembly includes approximately 2.6 Gb of
sequence on chromosomes 1-19, X, Y, M (mitochondrial DNA)
and Un (unmapped clone contigs).
For in-depth information about the process used to assemble this version, see
the NCBI website.
On chromosome Y in this assembly, only the short arm has
reliable mapping data; therefore, most of the contigs on
the Y chromosome are unplaced.
Note that the UCSC mm8 database contains only the
reference strain C57BL/6J.
The mm8 sequence and annotation data may be downloaded
from the Genome Browser
FTP
server or
Downloads
web page. The mm8 annotation tracks were generated by UCSC
and collaborators worldwide.
We'd like to thank Deanna Church and the Mouse Genome
Sequencing Consortium for this assembly. We'd also like to
acknowledge the work of the UCSC mm8 team: Hiram Clawson,
Fan Hsu, Kayla Smith, Ann Zweig, Robert Kuhn, Brooke
Rhead, Archana Thakkapallayil, and Donna Karolchik.
For a complete list
of the individuals and organizations who participated
in this assembly, see the
Credits
page.
14 April 2006 - NCBI Build 36.1 Human Reference Sequence Available in Browser
The latest human genome reference sequence assembly (NCBI
Build 36.1, March 2006) is now available as database hg18 in
the UCSC Genome Browser. This sequence, which was obtained
from NCBI, was produced by the
International Human Genome Sequencing Consortium.
The hg18 assembly contains four alternate haplotype regions:
chr22_h2_hap1 -- an alternate chromosome 22 assembly that
contains the CYP2D6 gene (NT_113959.1). CYP2D6 is deleted
in the reference assembly.
chr5_h2_hap1 -- a chromosome 5 alternate assembly of the
SMN1 gene region (NT_113801.1, NT_113802.1).
chr6_cox_hap1 -- an A1-B8-DR3 alternate haplotype assembly
of the chromosome 6 MHC region based on sequence data from
the COX library (NT_113891.1).
chr6_qbl_hap2 -- an A26-B18-DR3 alternate haplotype assembly
of the chromosome 6 MHC region based on sequence data from
the QBL library (NT_113892.1, NT_113893.1, NT_113894.1,
NT_113895.1, NT_113896.1, NT_113897.1).
The Y chromosome in this assembly contains two
pseudoautosomal regions (PARs) at chrY:1-2709520 and
chrY:57443438-57772954. These sequences were taken from
the corresponding regions in the X chromosome and are exact
duplications of the X chromosome sequences.
Bulk downloads of the data are available from the UCSC
downloads server via
ftp or
http. We recommend that you
use ftp or rsync for downloading large or multiple files.
We'd like to thank NCBI and the International Human Genome
Sequencing Consortium for furnishing the data, and the
entire UCSC Genome Browser staff for contributing to this
release. Fan Hsu led the UCSC engineering effort; QA was
headed up by Ann Zweig.
6 March 2006 - Purple Sea Urchin Genome Assembly Available in Genome Browser
The April 2005 release of the Purple Sea Urchin genome
(Strongylocentrotus purpuratus) is now available
in the UCSC Genome Browser. This assembly, UCSC version
strPur1, was produced by the Baylor College of Medicine
Human Genome Sequencing Center (BCM HGSC) and corresponds
to their Spur_0.5 whole genome shotgun assembly.
This release was assembled from whole genome shotgun reads
using the Atlas genome assembly system at the BCM HGSC.
Several whole genome shotgun libraries, with inserts of 2-6
kb, were used to produce the data. About 7 million reads
were assembled, representing about 800 Mb of sequence and
about 6x coverage of the (clonable) sea urchin genome.
Highly repeated sequences were assembled separately into
reptigs and merged into the genome assembly. Sequences from
BAC clones were omitted from this assembly and will be
placed in a subsequent version of the draft sequence.
This is a draft sequence and may contain errors; therefore,
users should exercise caution. Typical errors in draft
genome sequences include misassemblies of repeated
sequences, collapses of repeated regions, and unmerged
overlaps (e.g. due to polymorphisms) creating
artificial duplications. However, base accuracy in contigs
(contiguous blocks of sequence) is usually very high with
most errors near the ends of contigs.
Bulk downloads of the sequence and annotation data are
available via the Genome Browser
FTP server
or the Downloads
page. These data have
specific conditions for use. The strPur1
annotation tracks were generated by UCSC and collaborators
worldwide. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
27 February 2006 - Upcoming Genome Browser Seminars in Texas, Florida and Washington, DC
The UCSC Bioinformatics Group announces four regional
seminars and hands-on computer workshops on the UCSC
Genome Browser, presented by
OpenHelix:
Houston, TX -- Tuesday, 14 March
Austin, TX -- Wednesday, 15 March
Washington, DC -- Tuesday, 18 April
Miami, FL -- Wednesday, 19 April
Two sessions will be offered each day: 9:00 a.m. to noon and
1 p.m. to 4 p.m.
These introductory sessions are geared towards anyone with a
basic knowledge of genomic and biological concepts who is
interested in learning how to use the UCSC Genome Browser.
No programming experience is required. The seminars will
cover the topics necessary to learn how to effectively use
the browser tool set, including basic Genome Browser
functionality, searching and BLAT use, Table Browser use,
creating and using custom annotation tracks, and an
introduction to the Gene Sorter. Lectures will be
accompanied by hands-on computer exercises conducted directly
on the Genome Browser web site. Participants receive a
complete set of slide and exercise handouts and printed
Quick Reference Cards.
For further information or to make a reservation, visit the
OpenHelix website or call 1-888-861-5051.
Register early; seating is limited. Academic and student
discounts are available.
17 February 2006 - Zebrafish Browser Updated
The latest zebrafish assembly -- Zv5 (UCSC version
danRer3, May 2005) -- is now available in the UCSC
Genome Browser and Blat server. The Zv5 assembly was
produced by
The Wellcome Trust Sanger Institute in collaboration with
the Max Planck Institute for Developmental Biology in
Tuebingen, Germany, and the Netherlands Institute for
Developmental Biology (Hubrecht Laboratory), Utrecht,
The Netherlands.
This assembly consists of 1,630,306,866 bp in 16,214
scaffolds (N50 = 1,116,981 bp) with a sequence coverage of
approximately 6.5-7x. The assembly has been tied to the
fingerprint contig map (data freeze 15th February, 2005)
and contains 699 Mb from 4,519 sequenced clones.
The danRer3 sequence and annotation data can be
downloaded from the UCSC Genome Browser
FTP server
or
downloads
page. Please review the
guidelines for using these data.
We'd like to thank the Wellcome Trust Sanger Institute,
the Max Planck Institute for Developmental Biology,
Hubrecht Laboratory and the other
institutions who contributed to the sequencing and
mapping effort of this release. Special thanks to the
Zebrafish Genome Initiative at Children's Hospital in
Boston for their collaboration on this release.
The UCSC zebrafish Genome Browser
was produced by Rachel Harte, Jennifer Jackson, Ann Zweig,
Ali Sultan-Qurraie, and Donna Karolchik. The
initial set of annotation tracks was generated by the
UCSC Genome Bioinformatics Group. See the
credits
page for a detailed list of the organizations and
individuals who contributed to the release of
this browser.
9 February 2006 - New Rhesus Macaque Browser Released
The latest rhesus macaque (Macaca mulatta) draft
assembly—v.1.0, Mmul_051212—is now available
in the UCSC Genome Browser. This version (UCSC rheMac2)
was sequenced and assembled by the Macaque Genome Sequencing
Consortium led by the Baylor College of Medicine Human
Genome Sequencing Center, in collaboration with the
Genome Sequencing Center at Washington University School of
Medicine in St. Louis and the J. Craig Venter Institute
Joint Technology Center.
The rhesus macaque follows the human and chimpanzee as the
third primate and first Old World monkey to have its genome
sequenced. Overall, the rhesus genome shares approximately
92 to 95 precent of its sequence with the human, compared
with the chimp at 98 precent. Because of its genetic,
physiologic, and metabolic similarities to the human and
chimp, the rhesus is an ideal reference point for
comparisons among the three primates.
The groups in the Macaque Genome Sequencing Consortium
produced preliminary assemblies of the genome data
using different and complementary approaches. The resulting
data were combined into a single, high-density
"melded" assembly by a team at J. Craig Venter
Institute. This collaboration made use of published rhesus
maps, the BAC fingerprint map from the Michael Smith Genome
Sciences Centre, and the human reference genome sequence.
The v.1.0 assembly covers about 93 percent of the rhesus
genome. For more information about the rheMac2 assembly,
see the Baylor
Rhesus Monkey Project web page.
The rheMac2 sequence and annotation data can be downloaded
from the UCSC Genome Browser
FTP
server or the
Downloads
page. These data have specific
conditions for use.
Many thanks to Baylor College of Medicine, the Macaque
Genome Sequencing Consortium, and the other
institutions who contributed to the sequencing and mapping
effort of the v.1.0 release. The UCSC Rhesus Genome
Browser was produced by Robert Baertsch, Kayla Smith,
Ann Zweig, Robert Kuhn, and Donna Karolchik. The initial
set of rheMac2 annotation
tracks was generated by the UCSC
Genome Bioinformatics Group. See the
credits
page for a detailed list of the organizations and
individuals who contributed to the release of this
browser.
18 January 2006 - D. sechellia Browser Released
The October 2005 D. sechellia assembly (UCSC
version droSec1) is now available in the UCSC Genome
Browser. This version was sequenced and assembled by the
Broad Institute of MIT and Harvard.
Downloads of the droSec1 data and annotations can be
obtained from the UCSC Genome Browser
FTP server or
Downloads page.
The initial set of droSec1 annotation tracks were generated
by UCSC.
Many thanks to the Broad Institute for providing the
sequence and assembly of this genome. The UCSC D.
sechellia Genome Browser was produced by Angie
Hinrichs, Kayla Smith and Donna Karolchik. See
the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
11 January 2006 - D. yakuba Browser Update
The latest D. yakuba assembly is now available in
the UCSC Genome Browser. This version — Release 2.0,
dated Nov. 2005 (UCSC version droYak2) — was sequenced
and assembled by the Genome Sequencing Center, Washington
University (WUSTL) School of Medicine in St. Louis.
The whole genome shotgun (WGS) assembly includes both raw
shotgun data and data from two rounds of
automated, directed read selection, which has improved the
sequence quality and narrowed or (in some instances) closed
gaps. For more assembly information and statistics,
see the WUSTL Genome Sequencing Center
Drosophila yakuba web page.
Downloads of the droYak2 data and annotations can be
obtained from the UCSC Genome Browser
FTP server or
Downloads page.
The initial set of droYak2 annotation tracks was generated
by UCSC.
Thanks to the Genome Sequencing Center at WUSTL School of
Medicine for providing the sequence and assembly of this
genome. The droYak2 Genome Browser was produced by Angie
Hinrichs, Jennifer Jackson and Donna Karolchik. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
4 January 2006 - D. persimilis Genome Browser Released
The UCSC Genome Bioinformatics Group has released a Genome
Browser and Blat server for the D. persimilis
genome. The Oct. 2005 release
(UCSC version droPer1) was sequenced and assembled by the
Broad Institute of MIT and Harvard.
The D. persimilis assembly joins nine other
Drosophila species featured in the UCSC Genome Browser.
Downloads of the droPer1 data and annotations can be obtained
from the UCSC Genome Browser
FTP server or
Downloads page.
The droPer1 annotation tracks were generated by UCSC and
collaborators worldwide.
Thanks to the Broad Institute for providing the sequence
and assembly of this genome. The UCSC D.
persimilis Genome Browser was produced by Angie
Hinrichs, Kayla Smith, Robert Kuhn, Jennifer Jackson and
Donna Karolchik. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
20 December 2005 - Dog Genome Browser Update Released
UCSC has updated the dog Genome Browser to include the
May 2005 v2.0 assembly (UCSC version canFam2) sequenced and
assembled by the Broad Institute of MIT and Harvard and
Agencourt Bioscience.
The whole genome shotgun sequence is
based on 7.6X coverage of the dog genome which includes
more than 98% of the euchromatic genome.
The dog genome, which contains approximately 2.5 billion
base pairs, is similar in size to the genomes of humans and
other mammals. The boxer breed was selected for the initial
sequencing effort, based on the lower variation rate in its
genome relative to other breeds. In addition to the boxer,
samples from several other dog breeds were used to generate
a set of single nucleotide polymorphisms (SNPs) to
facilitate disease studies.
The SNPs are available from the Broad Institute
dog SNP web page.
For more information about the dog draft assembly, see the
Broad Institute
Dog Genome Sequencing Project web page.
Many thanks to the Broad Institute of MIT and Harvard,
Agencourt Bioscience, and the other institutions who
contributed to the sequencing, assembly, and mapping
efforts. The canFam2 Genome Browser team included
Angie Hinrichs, Jennifer Jackson, and Donna Karolchik.
See the
credits
page for a detailed list of the organizations and
individuals who contributed to this release.
15 December 2005 - New Mouse Assembly Available in Genome Browser
The latest mouse genome assembly from the Mouse Genome
Sequencing Consortium, NCBI Build 35 (UCSC version mm7),
is now available in the UCSC Genome Browser.
The Build 35 assembly includes approximately 2.6 Gb of
sequence, of which about 2.2 Gb is finished
sequence. Chromosomes 2,
4, 11 and X are finished in this build. To review in-depth
statistics on the assembly, see the NCBI
Build 35 Data web page.
Please note that the UCSC mm7 database contains only the
reference strain C57BL/6J.
The mm7 sequence and annotation data may be downloaded
from the Genome Browser
FTP
server or
Downloads
web page. The mm7 annotation tracks were generated by UCSC
and collaborators worldwide.
We'd like to thank Deanna Church and the Mouse Genome
Sequencing Consortium for this assembly. We'd also like to
acknowledge the work of the UCSC mm7 team: Hiram Clawson,
Fan Hsu, Ann Zweig, Kayla Smith, Robert Kuhn
and Donna Karolchik.
For a complete list
of the individuals and organizations who participated
in this assembly, see the
Credits
page.
2 December 2005 - Announcing the VisiGene Image Browser
We are pleased to announce the release of a new software
tool in the Genome Browser collection, the
VisiGene Image Browser.
VisiGene offers the ability to view in situ images,
allowing examination of expression patterns at both
the tissue and cellular levels. The browser serves as a
virtual microscope that lets viewers retrieve images that
meet specific search criteria, then interactively zoom
and scroll across the collection.
The VisiGene Browser may be accessed from the menu on the
UCSC Genome Bioinformatics home page or through a link on
the details pages of Known Genes for which a VisiGene
annotation exists.
The initial release of VisiGene includes the following
image collections:
We'd like to thank the organizations listed above for
permitting us to add their images to the VisiGene database.
VisiGene was written by Jim Kent and Galt Barber of the
UCSC Genome Bioinformatics Group. Contact
Jim
if you have an image set you'd like to contribute for
display.
2 December 2005 - Allen Brain Atlas Annotation Added to Genome Browser
We have released a new annotation track — Allen Brain
Atlas Probes — that may be found in the Expression and
Regulation section of the latest mouse and human assemblies
(mm6 and hg17). The Allen Brain Atlas (ABA) is an extensive
database of high resolution in situ hybridization
images of adult male mouse brains covering the majority of
genes. This track provides a link to the ABA images for each
probe. For more information about the ABA, see the
description page that accompanies this track.
We'd like to thank the Allen Institute for Brain Science,
and Susan Sunkin in particular, for coordinating with UCSC
on this annotation.
17 October 2005 - UCSC Genome Browser Tutorial at ASHG 2005
OpenHelix will be presenting a one-hour seminar,
"Introduction to the UCSC Genome Browser", at the
American Society of Human Genetics (ASHG) 2005 meeting on
26 October, 6:30-7:30 p.m. The introductory tutorial
will cover the topics needed to effectively use the
Genome Browser, including basic search functionality and
BLAT use, Table Browser use, creating and using Custom
Tracks, and an introduction to the Gene Sorter. The class,
which is open to all registered ASHG attendees,
does not require programming skills, although a basic
knowledge of genomic and biological concepts is recommended.
The free tutorial will be conducted at the Grand America
Hotel, Audubon Room. Snacks and beverages will be served.
Attendees will receive a free download of training
materials. For further information, visit
www.openhelix.com or call 1-888-861-5051.
11 October 2005 - D. grimshawi Browser Now Available
The UCSC Genome Bioinformatics Group has added the
Drosophila grimshawi genome to the collection of
fly genomes available in the UCSC Genome Browser. This
assembly (UCSC version droGri1, Aug. 2005) was
produced by Agencourt Bioscience Corporation in
Beverly, MA, USA, using the Arachne assembler.
The droGri1 assembly contains 25,052 scaffolds ranging in
size from 196 bases to 14,170,260 bases.
Bulk downloads of the sequence and annotation data are
available via the Genome Browser
FTP server
or Downloads page. Please review the data use guidelines outlined in
the README.txt files that accompany the downloads. The
data use restrictions are also available on the Genome
Browser Credits
page.
We'd like to thank Agencourt Bioscience Corporation
for providing this assembly. The
UCSC droGri1 browser was produced by
Angie Hinrichs, Brian Raney, Jennifer Jackson, Kayla Smith
and Donna Karolchik. The UCSC Genome Bioinformatics Group
generated the initial set of annotation tracks. See the
Credits page for
a detailed list of the organizations and individuals who
contributed to this release.
7 October 2005 - New D. ananassae Browser Released
The UCSC Genome Bioinformatics Group has updated the
Drosophila ananassae Genome Browser to the
1 August, 2005 assembly. This version (UCSC version droAna2)
was produced by Agencourt Bioscience Corporation using the
Arachne assembler.
The assembly contains 13,772 scaffolds ranging in size from
55 bases to 23,697,768 bases, with a mean size of 16822.3
and median of 1537.
Sequence and annotation data for the droAna2 assembly can be
downloaded from the UCSC Genome Browser
FTP server
or
downloads
page. Please review the data use guidelines outlined in
the README.txt files that accompany the downloads. The
data use restrictions are also available on the Genome
Browser credits
page.
We'd like to thank Agencourt Bioscience Corporation for this
assembly. The UCSC droAna2 browser was produced by
Angie Hinrichs, Brian Raney, Ann Zweig, Kayla Smith and
Donna Karolchik. The UCSC Genome Bioinformatics Group
generated the initial set of annotation tracks. See the
credits
page for a detailed list of the organizations and
individuals who contributed to this release.
4 October 2005 - Updated Cow Browser Available
The UCSC Genome Bioinformatics Group has released a
Genome Browser and Blat server for the Mar. 2005 Btau_2.0
draft assembly of the cow genome. This assembly (UCSC
version bosTau2) was provided by Baylor
College of Medicine Human Genome Sequencing Center in
Houston, TX.
The Btau_2.0 release was assembled from whole genome
shotgun (WGS) reads using the Atlas genome assembly
system. Several WGS libraries, with inserts of 2 - 4 kb
and 4 - 6 kb, were used to produce the data.
Approximately 23 million reads were assembled, representing
about 17.7 Gb of sequence and 6.2x coverage of the
(clonable) bovine genome. Highly repeated sequences and
BAC clones sequences were omitted from this assembly; these
will be placed in a subsequent version of the draft
sequence. The assembly contains chromosomes 1-29, X, M, and
Bin0, as well as 98058 scaffolds. For details about
changes UCSC made to the assembly format for display
purposes, please see the bosTau2 Genome Browser
gateway page.
More information on the Btau_2.0 assembly can be found on
the Baylor
Bovine Genome Project web page.
Bulk downloads of the sequence and annotation data are
available via the Genome Browser
FTP server or
Downloads
page. Please refer to the Baylor
conditions of use regarding these
data. The bosTau2 annotation tracks were generated by
UCSC and collaborators worldwide.
We'd like to thank Baylor College of Medicine for
the bovine sequence and assembly. We'd also like to
acknowledge the members of the UCSC Genome Bioinformatics
Group who contributed to the Cow Genome Browser:
Galt Barber, Brian Raney, Mark Diekhans, Jennifer Jackson
and Donna Karolchik. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
20 September 2005 - Three Drosophila Assemblies Released in Genome Browser
The UCSC Genome Bioinformatics Group has added three more
Drosophila genomes to the collection of fly genomes in
the UCSC Genome Browser. The new
genomes, which include the initial assembly of D.
erecta (droEre1, Aug. 2005) and the updated assemblies
of D. virilis (droVir2, Aug. 2005) and D.
mojavensis (droMoj2, Aug. 2005), were
produced by Agencourt Bioscience Corporation in
Beverly, MA, USA. All three genomes were assembled using
the Arachne assembler.
The droEre1 assembly contains 5,124 scaffolds ranging in
size from 154 bases to 26,647,023 bases, with a mean size
of 29832.7 and median of 1740.
The droVir2 assembly consists of 13,562 scaffolds ranging in
size from 57 bases to 25,269,527 bases, with a mean size of
15263.1 and median of 1249.
The droMoj2 assembly is comprised of 6,843 scaffolds ranging
in size from 101 bases to 34,172,700 bases, with a mean size
of 28389.6 and median of 1671.
Bulk downloads of the sequence and annotation data are
available from the UCSC downloads server:
Please review the data use guidelines outlined in
the README.txt files that accompany the downloads. The
data use restrictions are also available on the Genome
Browser credits
page.
We'd like to thank Agencourt Bioscience Corporation
for providing these assemblies. The
UCSC Drosophila browsers were produced by
Angie Hinrichs, Brian Raney, Jennifer Jackson and Donna
Karolchik. The UCSC
Genome Bioinformatics Group generated the initial set
of annotation tracks. See the
credits page for
a detailed list of the organizations and individuals who
contributed to this release.
9 September 2005 - C. intestinalis v2.0 Genome Browser Released
The v2.0 C. intestinalis draft assembly from the
US DOE Joint Genome Institute (JGI) is now available
in the UCSC Genome Browser and Blat server (UCSC database
ci2).
This whole genome shotgun assembly was constructed with
the JGI assembler, JAZZ, using paired-end sequencing reads.
Starting with a coverage of 11x, additional data --
including BAC and FISH markers -- were used to map scaffolds
to chromosome arms. The size of this assembly, including
unmapped scaffolds, is 173 Mb, with 94 Mb of the sequence
mapped to chromosome arms.
Bulk downloads of the sequence and annotation data are
available via the Genome Browser
FTP server or
Downloads page. The ci2 annotation tracks
were generated by UCSC and collaborators worldwide. See the
Credits page for a
detailed list of the organizations and
individuals who contributed to this release.
Many thanks to the JGI and their collaborators for providing
the v2.0 sequence and annotations. The ci2 Genome Browser
was produced by Brian Raney, Mark Diekhans, Ann Zweig,
Kayla Smith, Robert Kuhn and Donna Karolchik.
11 August 2005 - Upcoming Genome Browser Seminars - San Francisco, Seattle, Chicago, Boston, Philadelphia, Atlanta
The UCSC Bioinformatics Group announces six regional
seminars and hands-on computer workshops on the UCSC
Genome Browser, presented by
OpenHelix:
San Francisco -- Monday, 22 August
Seattle -- Wednesday, 24 August
Chicago -- Tuesday, 27 September
Boston -- Wednesday, 28 September
Philadelphia -- Tuesday, 15 November
Atlanta -- Wednesday, 16 November
These introductory sessions are geared towards anyone with a
basic knowledge of genomic and biological concepts who is
interested in learning how to use the UCSC Genome Browser.
No programming experience is required. The seminars will
cover the topics necessary to learn how to effectively use
the browser tool set, including basic Genome Browser
functionality, searching and BLAT use, Table Browser use,
creating and using custom annotation tracks, and an
introduction to the Gene Sorter. Lectures will be
accompanied by hands-on computer exercises conducted directly
on the Genome Browser web site.
For location and registration information, visit the
OpenHelix website or call 1-888-861-5051.
Academic and student discounts are available.
Posted on 13 June 2005 - Drosophila simulans Genome Browser Released
The UCSC Genome Bioinformatics Group has released a
Genome Browser for the Drosophila simulans draft
genome sequence. The Release 1.0 assembly (UCSC version
droSim1, April 2005) was produced by the
Genome
Sequencing Center at the Washington University in St.
Louis (WUSTL) School of Medicine. Release 1.0 represents
a composite of several different D. simulans
lines: contigs from the w501 line comprise the primary
scaffolding, with contigs and unplaced reads from six
other lines used to fill gaps in the w501 assembly.
The total size of this assembly, excluding the gapless
14,972 bp mitochondrial sequence, is 142,405,747 bp
including gaps and 127,241,461 bp excluding gaps. For
more information about the D. simulans assembly
and statistics, see the WUSTL Genome Sequencing Center
Drosophila simulans web page.
Downloads of the droSim1 data and annotations may be
obtained from the UCSC Genome Browser
FTP server or
Downloads page. The droSim1 annotation
tracks were generated by UCSC and collaborators worldwide.
Thanks to the Genome Sequencing Center, WUSTL School of
Medicine for providing this assembly. We'd also like to
acknowledge the UCSC team who worked on this release:
Angie Hinrichs, Jennifer Jackson, Ali Sultan-Qurraie,
Brian Raney and Donna Karolchik. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
Posted on 31 May 2005 - June Genome Browser Seminars in San Diego, CA and Salt Lake City, UT
The UCSC Bioinformatics Group announces two seminars and
hands-on workshops on the UCSC Genome Browser, presented by
OpenHelix,
a bioinformatics training, software testing and consulting
company.
These introductory sessions are geared towards anyone with a
basic knowledge of genomic and biological concepts who is
interested in learning how to use the UCSC Genome Browser.
No programming experience is required. The seminars will
cover the topics necessary to learn how to effectively use
the browser tool set, including basic Genome Browser
functionality, searching and BLAT use, Table Browser use,
creating and using custom annotation tracks, and an
introduction to the Gene Sorter. Lectures will be
accompanied by hands-on computer exercises conducted directly
on the Genome Browser web site.
The first three-hour course will be held on Thursday
9 June in the Salt Lake City, UT area. Two sessions will
be offered: 9am-12pm and 1pm-4pm.
The second seminar will be held in San Diego, CA
on Friday, 10 June. Two sessions
will be offered: 9am-12pm and 1pm-4pm.
For registration information, visit the
OpenHelix website or call 1-888-861-5051.
Academic and student discounts are available.
Posted on 18 May 2005 - Rhesus Monkey Genome Browser Released
The UCSC Genome Bioinformatics group has released a
Genome Browser for the rhesus monkey draft assembly,
Mmul_0.1 (UCSC version rheMac1), produced by the
Baylor College of Medicine Human Genome Sequencing Center
in collaboration with J. Craig Venter Science Foundation
Joint Technology Center and the Genome
Sequencing Center at Washington University School of
Medicine in St. Louis.
This Old World monkey, which is a primate model organism,
is important for the study of human biology and disease
due to its genetic, physiologic and metabolic
similarities to humans.
Mmul_0.1 is a preliminary assembly using whole genome
shotgun (WGS) reads from small and medium insert clones.
Approximately 14.6 million reads were used in the
assembly, representing about 12.6 Gb of sequence and
about 4.6x coverage of the (clonable) genome.
The total length of all contigs is
approximately 2.7 Gb, or 2.8 Gb including gaps between
contigs.
Highly-repeated sequences and sequences from BAC clones
were omitted from this assembly and will be placed in a
subsequent version of the draft sequence.
For more information about the rheMac1 assembly, see the
Baylor
Rhesus Monkey Project web page.
The rheMac1 sequence and annotation data can be downloaded
from the UCSC Genome Browser
FTP
server or the
Downloads
page. These data have specific
conditions for use.
Many thanks to Baylor College of Medicine, the Rhesus
Monkey Genome Sequencing Consortium, and the other
institutions who contributed to the sequencing and mapping
effort of the Mmul_0.1 release. The UCSC Rhesus Genome
Browser was produced by Robert Baertsch, Galt Barber,
and Donna Karolchik. The initial set of rheMac1 annotation
tracks was generated by the UCSC
Genome Bioinformatics Group. See the
credits
page for a detailed list of the organizations and
individuals who contributed to the release of this
browser.
Posted on 5 May 2005 - New Mouse Assembly Available in Genome Browser
The latest mouse genome assembly from the Mouse Genome
Sequencing Consortium, NCBI Build 34 (UCSC version mm6),
is now available in the UCSC Genome Browser. In
conjunction with this release, we have archived mouse
assemblies mm3 and mm4. All archived assemblies are
available for download via our
downloads server.
The Build 34 assembly has an assembled length of
approximately 2.6 Gb, of which about 1.9 Gb is finished
sequence. Chromosomes 2,
4, 11 and X are finished in this build. To review in-depth
statistics on the assembly, see the NCBI
Build 34 Data web page.
NOTE: In the Genome Browser mm6 assembly,
chrY_random erroneously contains a region duplicated from
chrY. For more information about this issue, see the
Genome Browser
FAQ. Please
also note that the UCSC mm6 database contains only the
reference strain C57BL/6J.
The mm6 sequence and annotation data may be downloaded
from the Genome Browser
FTP
server or
Downloads
web page. The mm6 annotation tracks were generated by UCSC
and collaborators worldwide.
Mirror sites, please note: due to the size of the
comparative genomics annotations in this assembly, the
data set requires an unusually large amount of disk space.
If you regularly download updates of the mouse data to
your site, you may want to examine your available disk
space before adding the annotation database from this
assembly and/or reschedule your download for a period of
low activity on your server. The size of the mm6
annotation database directory
($WEBROOT/goldenPath/mm6/database/) is
approximately 93 GB. Including the related net and chains,
the total size is 124 GB.
We'd like to thank Deanna Church and the Mouse Genome
Sequencing Consortium for this assembly. We'd also like to
acknowledge the work of the UCSC mm6 team: Hiram Clawson,
Fan Hsu, Jennifer Jackson, Robert Kuhn, Ali
Sultan-Qurraie, Heather Trumbower and Donna Karolchik.
For a complete list
of the individuals and organizations who participated
in this assembly, see the
Credits
page.
Posted on 2 May 2005 - Archiving mm3 and mm4 assemblies
To make room for the NCBI Build 34 mouse assembly (mm6,
March 2005), we are archiving the mm3 and mm4 mouse
assemblies. These assemblies will remain available for download on our
downloads
server, although blat will no longer be supported.
We plan to release the mm6 assembly in the next day or so.
Posted on 24 Mar. 2005 - Genome Browser Tutorial at Experimental Biology 2005 on 5 April
OpenHelix will be presenting a one-hour introductory
seminar on the UCSC Genome Browser at the
Experimental Biology 2005 meeting on 5 April, 5:00-6:00.
The tutorial will cover the topics needed to effectively
use the Browser, including basic functionality, searching
and BLAT use, Table Browser use, creating and using Custom
Tracks, and an introduction to the Gene Sorter.
The free session will be conducted at the San
Diego Convention Center, Room 12. For further information,
visit the OpenHelix website or call
1-888-861-5051.
OpenHelix will also be presenting brief introductory
overviews of the UCSC Genome Browser in its Experimental
Biology booth #133-135 during show hours. Stop by the
booth for more information and to receive your free UCSC
Quick Reference Card.
Posted on 2 Mar. 2005 - CCDS Data Set Released
The initial results from the Consensus Coding Sequence
project (CCDS) were released to the public today.
CCDS is a collaborative effort to identify a core set of
human protein-coding regions that are consistently
annotated and of high quality.
The initial CCDS data set,
containing nearly 15,000 transcripts, has been posted on three
Internet sites: the
UCSC Genome Browser,
the Ensembl Browser and the
NCBI CCDS Database website.
The genes may be viewed on the UCSC hg17 (May 2004)
Human Genome Browser in the CCDS annotation track
located in the Genes and Gene Prediction Tracks section.
The CCDS gene set is built by consensus among the
following collaborating organizations:
Each gene in the CCDS set is assigned a unique identifier
and version number, e.g. CCDS234.1. The version number
will be updated if either the CDS structure or the
underlying genome sequence at that location changes. The
CCDS set will be mapped forward, with identifiers
preserved, when the annotations or sequence update.
Changes to existing CCDS genes will be done by
collaboration agreement; no single group will change the
set unilaterally. CCDS identifiers are included on
relevant NCBI RefSeq and Entrez Gene records.
Gene structure information is obtained from both curated
and automated genes sources. The primary curation groups
are the Havana team at the WTSI and the
RefSeq annotation group at NCBI. In
addition, manually curated information on chr14
(Genoscope) and Chr7 (WUSTL) has been included from the
Vega
database. The Ensembl group and the RefSeq
computational pipeline provide the automated data. Curated
information is favored over automated information; the
information must be consistent between the Hinxton
(Vega/Ensembl) and NCBI groups and also pass UCSC's
stringent QC requirements.
At a minimum, a gene must meet three quality criteria
to be included in the CCDS set:
The coding region has a full-length annotation with
an initiating ATG, a valid stop codon, and no in-frame
stop codons.
Protein can be translated from the genome without
frameshifts.
Consensus splice-sites are used.
For more information on the process used to identify and
evaluate CCDS genes, refer to the description page for
the Genome Browser CCDS track. The number and type of
quality tests performed may be expanded in the future,
but includes analysis to identify putative pseudogenes,
retrotransposed genes, consensus splice sites, supporting
transcripts, and protein homology.
The completeness of the CCDS gene set should improve as
the curation and automated annotation processes mature
and additional experimental validation is obtain for
weakly-supported genes.
UCSC would like to thank EBI, NCBI and WTSI for their
collaboration in the release of these data.
We would also like to acknowledge the efforts of the
UCSC staff who worked on this project: Mark Diekhans,
Robert Baertsch, Adam Siepel, Fan Hsu, and Robert Kuhn.
Posted on 24 Feb. 2005 - Genome Browser Training - St. Louis and NYC
We'd like to announce upcoming UCSC Genome Browser
seminars and hands-on computer workshops in St. Louis, MO,
and New York, NY, presented by OpenHelix, the
bioinformatics training, software testing and consulting
company.
These introductory tutorials will cover the topics
needed to effectively use the browser, including basic
functionality of Genome Browser searching and BLAT use,
Table Browser use, creating and using Custom Tracks, and
an introduction to the Gene Sorter.
The St. Louis class will be held on 29 March, 2005 at
the Object Computing, Inc. training
center. Two sessions will be offered: 9 a.m. - 12 p.m.
and 1 - 4 p.m.
The New York City class will be held on 30 March, 2005 at
the
ThinkPath Training facility. Two
sessions will be offered: 9 a.m. - 12 p.m. and
1 - 4 p.m.
For more information about class locations, costs, and
registration, visit the
OpenHelix website or call
1-888-861-5051. Academic, student, and early registration
discounts are available.
Posted on 23 Feb. 2005 - New Honeybee Genome Browser
The UCSC Genome Bioinformatics group has released a
Genome Browser for a second honeybee assembly, Amel_2.0
(UCSC version apiMel2), produced by the Baylor College of
Medicine Human Genome Sequencing Center.
The assembly -- which is approximately 229 Mb in size
including contig gaps -- was sequenced using a combined
whole genome shotgun (WGS) and BAC clone approach.
Overall sequence coverage is estimated at 7.5x.
In this assembly, scaffolds have been arranged into 17
linkage groups that are somewhat equivalent to
chromosomes. For more information about the assembly,
see the Baylor
honeybee project website.
The apiMel2 sequence and annotation data can be
downloaded from the UCSC Genome Browser
FTP server
or
downloads
page. Please see the Baylor
conditions of use page for guidelines
regarding the use of these data.
Many thanks to Baylor College of Medicine and the other
institutions who contributed to the sequencing and
mapping effort of the Amel_v2.0 release. The UCSC
A. mellifera Genome Browser
was produced by Andy Pohl, Angie Hinrichs, Jennifer
Jackson, and Donna Karolchik. The initial set of apiMel2
annotation tracks was generated by the UCSC Genome
Bioinformatics Group. See the
credits
page for a detailed list of the organizations and
individuals who contributed to the release of
this browser.
Posted on 17 Feb. 2005 - Cow Genome Browser Released
The UCSC Genome Bioinformatics Group has released a
Genome Browser and Blat server for the Sep. 2004 Btau_1.0
draft assembly of the cow genome. This assembly (UCSC
version bosTau1) was provided by Baylor
College of Medicine Human Genome Sequencing Center in
Houston, TX.
The Btau_1.0 release was assembled from whole genome
shotgun (WGS) reads using the Atlas genome assembly
system. Several WGS libraries, with inserts of 2 - 4 kb
and 4 - 6 kb, were used to produce the data. Approximately
15 million reads were assembled, representing about 9 Gb
of sequence and 3x coverage of the (clonable) bovine
genome. Highly repeated sequences and BAC clones sequences
were omitted from this assembly; these will be placed in a
subsequent version of the draft sequence. The assembly
contains approximately 450,000 scaffolds.
For more information on the Btau_1.0 assembly, see the
Baylor
Bovine Genome Project web page.
Bulk downloads of the sequence and annotation data are
available via the Genome Browser
FTP server or
Downloads
page. Please refer to the Baylor
conditions of use regarding these
data. The bosTau1 annotation tracks were generated by
UCSC and collaborators worldwide.
We'd like to thank Baylor College of Medicine for
the bovine sequence and assembly. We'd also like to
acknowledge the members of the UCSC Genome Bioinformatics
Group who contributed to the Cow Genome Browser:
Heather Trumbower, Jim Kent, Hiram Clawson, Angie
Hinrichs, Brian Raney, Mark Diekhans, Robert Kuhn, Ali
Sultan-Qurraie, and Donna Karolchik. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
Posted on 15 Feb. 2005 - UniProt (Swiss-Prot/TrEMBL) Display Changes
We have made several adjustments to the Genome
Browser databases to accommodate recent changes to display
IDs introduced by UniProt (aka Swiss-Prot/TrEMBL). If you
are using the proteinID field in our knownGene table or
the Swiss-Prot/TrEMBL display ID for indexing or
cross-referencing other data, we strongly suggest you
transition to the UniProt accession number. These changes
will also affect anyone who is mirroring our site.
To review a detailed list of the changes to the Genome
Browser databases, see our
FAQ.
Posted on 14 Feb. 2005 -D. melanogaster Release 4 Now Available
The D. melanogaster Release 4 assembly (UCSC
version dm2, Apr. 2004) is now available in the
Genome Browser. This version includes Release 4
euchromatic sequence from the Berkeley Drosophila Genome
Project (BDGP), Release 3.2 heterochromatic
genome sequence from the Drosophila Heterochromatin Genome
Project (DHGP), and Release 4.0 annotations
(dated Nov. 2004) from FlyBase. Insects in the UCSC
Genome Browser collection include six Drosophila
genomes, the honeybee, and Anopheles gambiae.
The Release 4 euchromatic sequence, 118.4 Mb in size,
contains six euchromatic chromosome arms with a total
of 23 sequence gaps. The assembly was validated in
collaboration with the Genome Sciences Centre at the
British Columbia Cancer Agency in Vancouver, Canada,
using fingerprint analysis of a tiling path of BACs
spanning the genome.
The Release 3.2 heterochromatic sequence is based on
20.7 Mb of Release 3 whole genome shotgun scaffolds
from Celera that could not be assembled into the
euchromatin arms, as well as a few BDGP-sequenced
scaffolds. The scaffolds have been assigned to
chromosomes where possible.
Downloads of the dm2 data and annotations may be obtained
from the UCSC Genome Browser
FTP server or
Downloads
page. The dm2 annotation tracks were provided by
FlyBase or generated by UCSC.
Thanks to BDGP, DHGP, and the Flybase Consortium for
providing the sequence, assembly, gene annotations and
analysis of this genome. The UCSC Genome Browser team
is Angie Hinrichs, Brian Raney, Galt Barber, and
Donna Karolchik. See the
Credits
page for a detailed list of the organizations and
individuals who contributed to this release.
Posted on 18 Jan. 2005 - Opossum Genome Browser
The opossum (Monodelphis domestica) is the latest
vertebrate addition to the UCSC Genome Browser genome
collection. The Oct. 2004 preliminary assembly -- UCSC
version monDom1 -- was sequenced and assembled by
The Broad Institute, Cambridge, MA, USA.
This preliminary draft was assembled from 33,507,069
placed reads, and consists of 109,065 contigs containing
a total of 3,492,108,230 bases.
There are 3,563,247,205 total bases in the 19,348
scaffolds in the assembly, with 71,138,975 bases in
the gaps between contigs within the scaffolds. The
scaffolds range in size from 1,000 bases to 22,286,839
bases.
The monDom1 sequence and annotation data can be
downloaded from the UCSC Genome Browser
FTP server
or
downloads
page. Please review the
guidelines for using these data.
Many thanks to The Broad Institute for providing these
data. The UCSC opossum Genome Browser
was produced by Hiram Clawson, Galt Barber,
Ali Sultan-Qurraie, Brian Raney and Donna Karolchik. The
initial set of annotation tracks was generated by the
UCSC Genome Bioinformatics Group. See the
credits
page for a detailed list of the organizations and
individuals who contributed to the release of
this browser.
Posted on 23 Dec. 2004 - Updated Zebrafish Assembly (Zv4) Now Available
The latest zebrafish assembly -- Zv4 (UCSC version
danRer2, June 2004) -- is now available in the UCSC
Genome Browser and Blat server. The Zv4 assembly was
produced by
The Wellcome Trust Sanger Institute in collaboration with
the Max Planck Institute for Developmental Biology in
Tuebingen, Germany, and the Netherlands Institute for
Developmental Biology (Hubrecht Laboratory), Utrecht,
The Netherlands.
This assembly consists of 1,560,480,686 bp in 21,333
scaffolds with a sequence coverage of approximately 5.7x.
443 Mb of the assembly is from 2,828 finished clones
and 121 Mb is from 1,272 unfinished clones.
75% of the sequence was tied to the fingerprint
contig (FPC) map, which provided a template for placing
the unfinished sequence. The remaining sequence was
filled with whole genome shotgun (WGS) contigs using a
combination of sequence alignment and BAC end positions.
The WGS contigs used in this assembly were identical to
those used for the Zv3 assembly, but the FPC data and
its integration with the WGS data has been considerably
improved.
The
Sanger Institute notes that there is high level of
misassembly present in this release due to the large
amount of
polymorphism in the DNA source. Highly variable regions
within the genome posed assembly difficulties, most
likely because the sequences originated from different
haplotypes.
For more information about this assembly, see the Sanger
Institute web page for the
Danio rerio Sequencing Project.
In addition to the assembly improvements noted above, a
new zebrafish repeat library was used to mask repeats in
the danRer2 Genome Browser, resulting in a cleaner set of
alignments containing considerably less "noise".
The danRer2 sequence and annotation data can be
downloaded from the UCSC Genome Browser
FTP server
or
downloads
page. Please review the
guidelines for using these data.
We'd like to thank the Wellcome Trust Sanger Institute,
the Max Planck Institute for Developmental Biology,
Hubrecht Laboratory and the other
institutions who contributed to the sequencing and
mapping effort of this release. Special thanks to the
Zebrafish Genome Initiative at Children's Hospital in
Boston for their collaboration on this release.
The UCSC zebrafish Genome Browser
was produced by Rachel Harte, Mark Diekhans, Heather
Trumbower, Jennifer Jackson, and Donna Karolchik. The
initial set of annotation tracks was generated by the
UCSC Genome Bioinformatics Group. See the
credits
page for a detailed list of the organizations and
individuals who contributed to the release of
this browser.
Posted on 22 Dec. 2004 - UCSC Releases Honeybee Browser
The UCSC Genome Bioinformatics group has released a
Genome Browser for the Amel_1.2 honeybee assembly
produced by the Baylor College of Medicine Human Genome
Sequencing Center.
The assembly -- which is approximately 213 Mb in size
including contig gaps --
was sequenced using a combined whole genome shotgun (WGS)
and BAC clone approach. The BAC clone sequence was
produced following a pooled-array strategy. Overall
sequence coverage is estimated at 6X.
For more information about this assembly, see the Baylor
honeybee project website.
The honeybee genome is of interest to the agricultural
community, in addition to its role as a model organism in the
study of several human health issues, including immunity,
allergic reaction, antibiotic resistance, development,
mental health, longevity, and diseases of the X chromosome.
The honeybee is also interesting for its social and
behavioral traits.
The apiMel1 sequence and annotation data can be
downloaded from the UCSC Genome Browser
FTP server
or
downloads
page. Please see the Baylor
conditions of use page for guidelines
regarding the use of these data.
Many thanks to Baylor, Children's Hospital Oakland
Research Institute (CHORI), and the other
institutions who contributed to the sequencing and
mapping effort of the Amel_1.2 release. The UCSC
A. mellifera Genome Browser
was produced by Angie Hinrichs, Brian Raney, Robert Kuhn,
and Donna Karolchik. The initial set of apiMel1 annotation
tracks was generated by the UCSC Genome Bioinformatics
Group. See the
credits
page for a detailed list of the organizations and
individuals who contributed to the release of
this browser.
Posted on 15 Dec. 2004 - Three New Drosophila Assemblies in Genome Browser
The UCSC Genome Bioinformatics Group has added three more
Drosophila genomes to the UCSC Genome Browser. The new
genomes -- initial assemblies of D.
ananassae (droAna1, Jul. 2004), D. virilis
(droVir1, Jul. 2004), and D. mojavensis
(droMoj, Aug. 2004) -- join the D. melanogaster,
D. yakuba, and D. pseudoobscura genomes
already in the collection.
The D. virilis and D. mojavensis genomes
were sequenced and assembled by
Agencourt Bioscience Corporation using
the Arachne assembler. The Institute of Genomic
Research (TIGR) produced the D. ananassae
assembly using the Celera assembler. For more details
about an individual genome, refer to the Genome Browser
gateway
page associated with the assembly.
In upcoming months, UCSC plans to provide
several additions and enhancements to the
Drosophila browsers:
- additional Drosophila genomes, including
D. erecta and D. simulans
- updated versions of D. melanogaster and other
genomes
- multiple alignments of all fly assemblies from the
12-Drosophila project to D. melanogaster
Sequence and annotation data for all the
Drosophila assemblies can be
downloaded from the UCSC Genome Browser
FTP server
or
downloads
page. Please review the data use guidelines outlined in
the README.txt files that accompany the downloads. The
data use restrictions are also available on the Genome
Browser credits
page.
We'd like to thank Agencourt Bioscience Corporation,
TIGR, and other institutions who contributed to the
sequencing and mapping effort for these assemblies. The
UCSC Drosophila browsers were produced by
Angie Hinrichs, Brian Raney, Heather Trumbower,
Robert Kuhn, Galt
Barber, Jennifer Jackson, Ali Sultan-Qurraie, and Donna
Karolchik. The UCSC
Genome Bioinformatics Group generated the initial set
of annotation tracks. See the
credits page for
a detailed list of the organizations and individuals who
contributed to this release.
Posted on 3 Dec. 2004 - SNP Track for Build 35 (hg17) Assembly Released
UCSC has released the much-awaited SNP annotation track for the
Build 35 (hg17) Human Genome Browser. The SNP data were
obtained from dbSnp Build 123, the first dbSnp
release based on the latest human assembly.
In conjunction with the data release, we have made
several improvements to the graphical display of the
track.
Our users now have the ability to filter the SNP data
based on validation status,
functional class, variant class, average heterozygosity
and other features. Variants may be drawn in
user-selected colors to highlight additional details
in the graphical image. Also, the browser now displays all
SNP variants at the appropriate base width, rather than
as generic ticks.
Posted on 17 Nov. 2004 - X. tropicalis v.3.0 Released in Genome Browser
The v.3.0 Xenopus tropicalis assembly is now
available on the UCSC Genome Browser. This whole genome
shotgun assembly
(xenTro1, October 2004) was provided by the U.S. DOE
Joint Genome Institute (JGI).
Version 3.0 was constructed with the JGI assembler,
Jazz, using paired end sequencing reads at a coverage of
7.4X. After trimming for vector and quality, 19.1
million reads assembled into 27,064 scaffolds totaling
1.63 Gbp. Roughly half the genome is contained in 392
scaffolds, each of which is at least 1.2 Mb in length.
For more information about this assembly, see the JGI
X. tropicalis website.
The xenTro1 sequence and annotation data can be
downloaded from the UCSC Genome Browser
FTP server
or
downloads
page. Please see the JGI
data release policy for data use
guidelines.
Many thanks to JGI and the other
institutions who contributed to the sequencing and
mapping effort of the v. 3.0 release. The UCSC X.
tropicalis Genome Browser
was produced by Fan Hsu, Jim Kent, Heather Trumbower,
Hiram Clawson, Brian Raney, Galt Barber, Mark Diekhans,
Angie Hinrichs, and Donna Karolchik. The initial set of
xenTro1 annotation tracks was generated by the
UCSC Genome Bioinformatics Group. See the
credits
page for a detailed list of the organizations and
individuals who contributed to the release of
this browser.
Posted on 17 Nov. 2004 - Genome Browser Tutorial Offered at ASCB Meeting
OpenHelix will be presenting the tutorial
"Introduction to the UCSC Genome Browser"
at the American
Society for Cell Biology (ASCB) Annual Meeting in
Washington, D.C. on 5 Dec., 8:30 - 10:00 p.m. This
introductory session will cover the topics needed to
effectively use the Genome Browser, including basic
functionality of Genome Browser searching and BLAT use,
Table Browser use, creating and using Custom Tracks, and
an introduction to the Gene Sorter.
The free 1-1/2-hour tutorial will be conducted at the
Washington Convention Center, Room 206. OpenHelix will
also be presenting brief introductory overviews of the
UCSC Genome Browser in its ASCB booth #510-512 during
show hours. Stop by the booth for more information and
to receive your free UCSC Quick Reference Card.
For more information about the tutorial and other
services offered by OpenHelix, visit
www.openhelix.com or call
1-888-861-5051.
Posted on 8 Oct. 2004 - Updated Proteome Browser Released
UCSC has released v1.1 of the UCSC
Proteome Browser. This updated version includes the
following major enhancements:
direct access to a Proteome Browser gateway via the
"Proteome Browser" menu link
on the Genome Browser home page. The Proteome Browser gateway
page prompts the user for a protein ID or gene
symbol, then directly starts up the Proteome Browser,
eliminating the multiple Genome Browser steps required by
the previous release.
extended protein coverage that includes all proteins in
the Swiss-Prot/TrEMBL databases, rather than just the
human, mouse and rat protein sets included in the previous
version.
In addition to providing direct access to the Proteome
Browser, the v1.1 release preserves the existing tight
coupling between the Proteome Browser and the Genome Browser
for the human, mouse and rat genomes. Users may still
navigate between the Genome Browser Known Genes track and
the Proteome Browser for quick, easy access to
the details of a gene's genomic and proteomic
sequence structures.
The UCSC team who worked on the Proteome Browser update
includes Fan Hsu, Robert Kuhn, Donna Karolchik and Tom
Pringle. Please send comments or questions to our mailing
list at
genome@soe.ucsc.edu.
Posted on 5 Oct. 2004 - East Coast Genome Browser Seminars - Nov. 2004
The UCSC Bioinformatics Group announces two seminars and
hands-on workshops on the UCSC Genome Browser, presented by
OpenHelix,
a bioinformatics training, software testing and consulting
company.
These introductory sessions are geared towards anyone with a
basic knowledge of genomic and biological concepts who is
interested in learning how to use the UCSC Genome Browser.
No programming experience is required. The seminars will
cover the topics necessary to learn how to effectively use
the browser tool set, including basic Genome Browser
functionality, searching and BLAT use, Table Browser use,
creating and using custom annotation tracks, and an
introduction to the Gene Sorter. Lectures will be
accompanied by hands-on computer exercises conducted directly
on the Genome Browser web site.
The first three-hour course will be held on Tuesday 9 November
in the Washington, D.C. area. Two sessions will be
offered: 9am-12pm and 1pm-4pm.
The second seminar will be held in the Raleigh/Durham, N.C.
area on Wednesday, 10 November. Two sessions
will be offered: 9am-12pm and 1pm-4pm.
For registration information, visit the
OpenHelix website or call 1-888-861-5051.
Academic, student, and early registration discounts are
available.
Posted on 1 Oct. 2004 - UCSC Releases New Table Browser
We are pleased to announce the release of an enhanced version
of the UCSC Table Browser.
This new release sports several improvements and additions
over the previous Table Browser, including:
a new streamlined user interface
support for generating filters that include fields from multiple tables, including those from non-positional tables
an enhanced schema-viewing utility that displays all
tables associated with a track, as well as all tables linked
to a selected table
the ability to restrict queries to include only data from ENCODE regions
the addition of a GALA output option
an option to save large output results sets directly to a
file rather than displaying them in the Table Browser
The preliminary
User's Guide
will be enhanced in upcoming weeks to include examples of
many common Table Browser queries generated by our users.
The new version of the Table Browser was produced by
Jim Kent, Donna Karolchik, Heather Trumbower, Hiram Clawson,
and Robert Kuhn, and incorporates code from the
previous version written by Angie Hinrichs.
We'd like to thank Mary Mangan and others on the
OpenHelix staff for their feedback on early versions of this
software.
The older version of the Table Browser will remain available
for a limited time at
http://genome.ucsc.edu/cgi-bin/hgText. Please send feedback and questions to our
mailing list at
genome@soe.ucsc.edu.
Posted on 10 Sep. 2004 - T. nigroviridis Genome Now Available in Genome Browser
The Genoscope v7 Tetraodon nigroviridis genome
assembly is now available in the UCSC Genome Browser and
Blat server. This assembly, UCSC version tetNig1 dated
Feb. 2004, is the result of a collaboration between
Genoscope and the
Broad Institute of MIT and Harvard.
The v7 assembly was constructed using the whole genome shotgun
(WGS) approach, resulting in a sequence coverage of about
7.9X. The assembly contains 45,609 contigs and 25,773
scaffolds generated by the Arachne program and covers more
than 90% of the genome. Additional linking data were used to
build ultracontigs and to organize the assembly into
chromosomes. Genoscope estimates the size of the Tetraodon
genome to be about 385 Mb.
Downloads of the tetNig1 data and annotations may be obtained
from the UCSC Genome Browser
FTP server
or Downloads
page. These data have been freely
provided by Genoscope before publication with
specific conditions for use.
The initial set of annotation tracks were generated by
Genoscope and the UCSC Bioinformatics Group based on
data provided Genoscope. Tetraodon gene predictions
generated by Genoscope using
GAZE will be available in the Genome
Browser within a few weeks.
Many thanks to Genoscope and the Broad Institute of
MIT and Harvard for this genome assembly. The UCSC team who
produced this browser are Rachel Harte, Robert Kuhn,
Donna Karolchik, and the Genome Browser sysadmin team.
See the
Credits
page for a detailed list of the organizations and individuals
who contributed to this release.
Posted on 1 Sep. 2004 - Genome Browser Released for D. pseudoobscura Draft Assembly
The UCSC Genome Bioinformatics Group has released a Genome
Browser and Blat server for the Drosophila
pseudoobscura Freeze 1 draft assembly (Aug. 2003).
This assembly, UCSC version dp2, was
produced by the Human Genome Sequencing Center (HGSC) at
Baylor College of Medicine.
Freeze 1 is a whole genome shotgun assembly produced using
Baylor HGSC's assembly engine, Atlas. The assembly, which
provides approximately 7x coverage of the euchromatic portion
of the genome, contains 759 scaffolds. The scaffold N50 size
is 1,018,646 bp. The total scaffold size for this assembly
is 139.3 Mbp, with an average size of 184,465 bp. Due to an
assembly error, four large scaffolds "jumped" chromosomes.
These have been split into "A" and "B" parts in the
downloadable assembly files. See the gateway page for more
information.
Baylor HGSC has provided a
putative chromosome assignment
for the majority of larger scaffolds (> 90% of unique
sequence), based on conservation between the Muller elements.
Downloads of the dp2 data and annotations may be obtained
from the UCSC Genome Browser
FTP server
or Downloads
page. The initial set of annotation tracks were generated by
UCSC.
Many thanks to the Baylor HGSC for providing the genome
assembly data. The UCSC team who produced this browser are
Angie Hinrichs, Heather Trumbower, Robert Kuhn,
Donna Karolchik, and the Genome Browser sysadmin team.
See the
Credits
page for a detailed list of the organizations and individuals
who contributed to this release.
Posted on 30 Aug. 2004 - Genome Browser Seminars - Seattle and San Francisco
The UCSC Bioinformatics Group announces 2 seminars and
hands-on workshops on the UCSC Genome Browser, presented by
OpenHelix,
a bioinformatics training, software testing and consulting
company.
These introductory sessions are geared towards anyone with a
basic knowledge of genomic and biological concepts who is
interested in learning how to use the UCSC Genome Browser.
No programming experience is required. The seminars will
cover the topics necessary to learn how to effectively use
the browser tool set, including basic Genome Browser
functionality, searching and BLAT use, Table Browser use,
creating and using custom annotation tracks, and an
introduction to the Gene Sorter. Lectures will be
accompanied by hands-on computer exercises conducted directly
on the Genome Browser web site.
The first three-hour course will be held on Monday 4 October
in Kirkland, WA (Seattle area). Two sessions will be
offered: 9:00 a.m. - noon or 1 - 4 p.m.
The second seminar will be held in Cupertino (San
Francisco Bay Area) on Tuesday, 5 October. Two sessions
will be offered: 1 - 4 p.m. or 6 - 9 p.m.
For registration information, visit the
OpenHelix website or call 1-888-861-5051.
Academic, student, and early registration discounts are
available.
Posted on 10 Aug. 2004 - Genome Browser Released for A. gambiae Draft Genome
The UCSC Genome Bioinformatics Group has released a Genome
Browser and Blat server for the Anopheles gambiae
v. MOZ2 draft genome sequence (Feb. 2003). This assembly --
UCSC version anoGam1 -- was produced by the International
Anopheles Genome Project and downloaded from Ensembl.
The MOZ2 assembly is a 10x whole genome shotgun assembly.
The assembled portion of the genome is about 278 Mbp in
length with a total of 8,987 unique scaffolds, the largest
scaffold being 23.1 Mbp. Approximately 85% of the sequence
has been assigned to chromosomal locations. Chromosome arms
chr2L, chr2R, chr3L, chr3R, and
chrX are represented by 13, 49, 42, 28, and 10 large scaffolds
respectively. No scaffolds have yet been assigned to the Y
chromosome. The unassigned scaffolds, concatenated together
in arbitrary order, can be found in the artificial unknown
"chromosome" chrUn.
Downloads of the anoGam1 data and annotations may be obtained
from the UCSC Genome Browser
FTP server or
Downloads
page. The anoGam1 annotation tracks were generated by UCSC and
collaborators worldwide.
Many thanks to the International Anopheles Genome
Project and Ensembl for providing the sequence of this genome.
The UCSC team who produced this browser are Angie Hinrichs,
Galt Barber, Donna Karolchik, and sysadmins Paul Tatarsky and
Jorge Garcia. See the
Credits
page for a detailed list of the organizations and individuals
who contributed to this release.
Posted on 29 Jul. 2004 - Zebrafish Genome Assembly Zv3 Now Available in Genome Browser
The Zv3 Zebrafish genome assembly (UCSC version danRer1) is
now available on the UCSC Genome Browser and Blat server.
This assembly was produced by The Wellcome Trust Sanger
Institute, Hinxton, UK, in collaboration with the Max Planck
Institute for Developmental Biology in Tuebingen, Germany,
and the Netherlands Institute for Developmental Biology
(Hubrecht Laboratory), Utrecht, The Netherlands.
The Zv3 assembly consists of 1,459,115,486 bp in 58,339
supercontigs, with a sequence coverage of approximately
5.7X. This zebrafish assembly is the first to be tied to
the FPC map: 1,083,447,588 bp (74%) of the sequence were
mapped in this way. Please note that this is a preliminary
assembly; a high level of misassembly is present due to
polymorphisms in the DNA source.
For more information about this assembly, see the Sanger
Institute's
Danio rerio Sequencing Project
web page.
UCSC plans to release the Zv4 version of the zebrafish
assembly on the Genome Browser in Fall '04.
Downloads of the Zebrafish data and annotations can be
obtained from the UCSC
FTP site or
Downloads
page. The danRer1 annotation tracks were generated by
UCSC and collaborators worldwide. See the
Credits
page for a detailed list of the organizations and individuals
who contributed to the success of this release.
We'd like to thank The Wellcome Trust Sanger Institute
and their collaborators for providing this assembly. A special
thanks to Yi Zhou, Anthony DiBiase and Leonard Zon from the
Children's Hospital in Boston, MA, USA for their collaboration
on this release. The UCSC Zebrafish
Genome Browser team is Rachel Harte, Heather Trumbower, and
Donna Karolchik.
Posted on 23 Jul. 2004 - Latest Human Genome Reference Sequence Now in Browser
The latest human genome reference sequence (NCBI Build 35,
May 2004) is now available as database hg17 in the UCSC
Genome Browser and Blat server. This sequence was obtained
from NCBI and was produced by the International Human
Genome Sequencing Consortium.
Bulk downloads of the data are available via FTP at
ftp://hgdownload.cse.ucsc.edu/goldenPath/hg17
or through the Downloads link on this page. We recommend
that you use FTP rather than HTML for the download of large
or multiple files.
We'd like to thank NCBI and the International Human Genome
Sequencing Consortium for furnishing the data, and the UCSC
team members who contributed to this release: Hiram Clawson,
Terry Furey, Heather Trumbower, Robert Kuhn, Donna Karolchik,
Kate Rosenbloom, Angie Hinrichs, Rachel Harte, Jim Kent and
our sysadmin team Patrick Gavin, Jorge Garcia,
and Paul Tatarsky.
Posted on 23 Jul. 2004 - D. yakuba Added to Genome Browser
The UCSC Genome Bioinformatics Group has released a Genome
Browser and Blat server on a second species of fruitfly,
D. yakuba. The April 2004 Release 1.0 of this genome
(UCSC version droYak1) was sequenced and assembled by the
Genome Sequencing Center, Washington University (WUSTL)
School of Medicine in St. Louis.
D. yakuba is closely related to the model organism,
D. melanogaster, with which it shared a common
ancestor approximately 10 million years ago.
The D. yakuba genome is largely alignable to the
D. melanogaster genome, but differs sufficiently to
offer an interesting study of sequence divergence between
the two species. D. yakuba occupies a critical
intermediate position among several Drosophila species that
will facilitate evolutionary studies among the fruitflies.
For information about the D. yakuba assembly
and statistics, see the WUSTL Genome Sequencing Center
Drosophila yakuba web page.
Downloads of the droYak1 data and annotations can be obtained
from the UCSC Genome Browser
FTP server or
Downloads page.
The droYak1 annotation tracks were generated by UCSC and
collaborators worldwide.
Thanks to the Genome Sequencing Center at WUSTL School of
Medicine for providing the sequence and assembly of this
genome. The
UCSC D. yakuba Genome Browser was produced by Angie
Hinrichs, Michael Chalup, and Donna Karolchik. See the
Credits
page for a detailed list of the organizations and individuals
who contributed to the success of this release.
Posted on 16 Jul. 2004 - Genome Browser Released for Mouse Assembly NCBI Build 33
The latest mouse assembly -- Build 33 from NCBI (UCSC version
mm5) -- is now available via the UCSC Genome Browser and
Blat server. This assembly includes approximately
2.6 gigabases of sequence.
Chromosome 11 is finished in Build 33; the Sanger
Institute has provided a corresponding agp file.
The whole genome N50 for this assembly is 22.3 Mb, in comparison
to 17.7 Mb for the previous build.
Please note: the UCSC mm5 assembly contains only the
reference strain C57BL/6J.
This assembly is a composite version in which phase 3 High
Throughput Genome Sequence (HTGS) was merged with the
Mouse Genome Sequencing Consortium v3 Whole Genome Shotgun
Assembly (MGSCv3). The assembly was performed by NCBI using
a "combined" tiling path that was created
automatically for the most part, but was manually curated
in places. This facilitated the placement of finished
sequence in the context of the MGSCv3 assembly. Draft
sequence was not included in this build: the slight
increase in coverage gained by using this would have been
offset by the increase in build errors.
The mm5 sequence and annotation data may be downloaded from
the Genome Browser
FTP
server or
Downloads
web page. The mm5 annotation tracks were generated by UCSC
and collaborators worldwide.
We'd like to thank Deanna Church, Richa Agrawala, and
the Mouse Genome Sequencing Consortium
for this assembly. We'd also like to
acknowledge the work of the UCSC mm5 team: Fan Hsu,
Hiram Clawson, Angie Hinrichs, Heather Trumbower, Mark
Diekhans, Donna Karolchik and our systems
administrators Jorge Garcia, Patrick Gavin and Paul Tatarsky.
Posted on 15 Jul. 2004 - C. intestinalis v1.0 Released in Genome Browser
The v1.0 C. intestinalis draft assembly from the
US DOE Joint Genome Institute is now available for study
using the UCSC Genome Browser and Blat server (UCSC database
ci1).
The whole genome shotgun assembly was constructed with the
JGI assembler (JAZZ) paired-end
sequencing reads at a coverage of 8.2X. The draft contains
116.7 million bp of nonrepetitive sequence in 2,501 scaffolds
greater than 3 kb. 60 Mbp of this has been assembled into
117 scaffolds longer than 190 Kbp, and 85% of the assembly
(104.1 Mbp) is found in 905 scaffolds longer than 20 kb. The
assembly, gene modeling and analysis were performed at the
JGI.
Bulk downloads of the sequence and annotation data are
available via the Genome Browser
FTP server or
Downloads page. The ci1 annotation tracks
were generated by UCSC and collaborators worldwide. See the
Credits page for a detailed list of the organizations and
individuals who contributed to this release.
Many thanks to the JGI and their collaborators for providing
the v1.0 sequence and annotations. The ci1 Genome Browser
was produced by
Brian Raney, Galt Barber, Heather Trumbower, Robert Kuhn,
Donna Karolchik and the Genome Browser sysadmin team -
Patrick Gavin, Jorge Garcia, and Paul Tatarsky. We'd also
like to thank Tom Pringle for his technical input and Mark
Diekhans for his work on the incremental updates for this
release.
Posted on 14 Jul. 2004 - Genome Browser Released for Dog Draft Assembly v1.0
UCSC has released a Genome Browser and Blat server on the
July 2004 v1.0 dog genome sequenced and assembled by the
Broad Institute of MIT and Harvard and Agencourt Bioscience.
The whole genome shotgun (WGS) sequence is
based on 7.6X coverage of the dog genome, assuming a WGS
assembly size of 2.4 Gb. The assembly has an N50 contig
length of 123 kb and an N50 supercontig length of 41.6 Mb.
The dog genome, which contains approximately 2.5 billion
base pairs, is similar in size to the genomes of humans and
other mammals. The boxer breed was selected for the initial
sequencing effort, based on the lower variation rate in its
genome relative to other breeds. In addition to the boxer,
samples from nine other dog breeds, four wolves and a coyote
are being used to generate an initial set of single
nucleotide polymorphisms (SNPs) to facilitate disease studies.
The SNPs should be available soon from
dbSNP.
For more information about the dog draft assembly, see the
NHGRI
press release.
Many thanks to the Broad Institute of MIT and Harvard, NHGRI,
Agencourt Bioscience, Children's Hospital Oakland Research
Institute, Centre National de la Recherche Scientifique,
North Carolina State University, and Fred Hutchinson Cancer
Research Center for their contributions to the sequencing,
assembly, and mapping efforts. The initial canFam1
annotation track set, generated by the UCSC Genome
Bioinformatics Group, will soon be
supplemented by annotations from collaborators
worldwide. See the
credits page
for a detailed list of the organizations and individuals who
contributed to the success of this release.
Posted on 24 Jun. 2004 - ENCODE Project Featured in Genome Browser
We'd like to announce the release of UCSC Genome Browser
features tailored to the ENCODE project community, including
an
ENCODE-specific page to
highlight
the ENCODE contributors and their work, guidelines for data
submission, and a list of specific links to ENCODE regions
in the Genome Browser.
The initial resources include sequences
for the current human assemblies (hg16, hg15, hg13, and hg12),
sequence of the
comparative species from NISC, tools for coordinate
conversion between human assemblies, format descriptions for
data submission, and contact information for help with
submitting annotation data and analyses. Bulk downloads of
the sequence and annotations may be obtained from the ENCODE
Project
Downloads
page.
We'd like to thank NHGRI for their
support of this project and the various contributors of
annotations and analyses.
Posted on 10 Jun. 2004 - Genome Browser Training Workshop - Boston, MA
The UCSC Bioinformatics Group announces a seminar and hands-on
workshop on the UCSC Genome Browser, presented by
OpenHelix,
a bioinformatics training, software testing and consulting
company.
This introductory session is geared towards anyone with a
basic knowledge of genomic and biological concepts who is
interested in learning how to use the UCSC Genome Browser.
No programming experience is required. The seminar will
cover the topics necessary to learn how to effectively use
the browser tool set, including basic Genome Browser
functionality, searching and BLAT use, Table Browser use,
creating and using custom annotation tracks, and an
introduction to the Gene Sorter. The lecture will be
accompanied by hands-on computer exercises conducted directly
on the Genome Browser web site.
The three-hour course will be held at Tufts University School
of Medicine, 145 Harrison Street, Boston, MA, on Tuesday,
August 10th. Two sessions will be offered: 1 - 4 p.m. or
6 - 9 p.m. For registration information, visit the
OpenHelix website or call 1-888-861-5051.
Academic, student, and early registration discounts are
available.
Posted on 28 May 2004 - UCSC Family Browser Name Changed to UCSC Gene Sorter
What's in a name? In an effort to clarify the role of the
UCSC Family Browser, we have changed its name to the UCSC
Gene Sorter. We think this name better describes this tool,
which lets the user collect information on groups of genes
that may be related in many different ways. The Gene Sorter
provides a wealth of information on gene expression, protein
homology (both within and across species), GO terms, and
Pfam domains, cross links to many other databases, and much
more.
If you haven't already tried this tool, we encourage you to
give it a spin. You'll find it at
http://genome.ucsc.edu/cgi-bin/hgNear,
or click the "Gene Sorter" link on any Genome Browser menu
bar.
Posted on 27 May 2004 - New Genome Browser Downloads Server
As a follow-up to last week's FTP site switch, we are changing
the location of the UCSC Genome Browser downloads site to
http://hgdownload.cse.ucsc.edu/.
All downloadable files currently located in
http://genome.ucsc.edu/goldenPath
will be moved to the new server.
Please make a note of the new URL and update any references
to it. Users accessing downloads through the Genome Browser
Downloads page
will be redirected automatically to the new location.
Posted on 19 May 2004 - New Genome Browser FTP Server
We have changed the URL for the UCSC Genome Browser ftp site
to ftp://hgdownload.cse.ucsc.edu/.
This replaces the old URL of ftp://genome.ucsc.edu/.
The old URL will be disabled within a few days.
Please make a note of the new URL and update any references
to it.
Posted on 11 May 2004 - C. elegans WS120 Added to Genome Browser
UCSC has released a Genome Browser and Blat server on an
updated version of the C. elegans genome. The
March 2004 assembly -- UCSC version ce2 -- is based on
sequence version WS120 deposited into
WormBase
as of 1 March 2004. This assembly has a finishing error rate
of 1:10,000.
The ce2 sequence and annotation data may be downloaded from
the Genome Browser
FTP server
or Downloads web page.
The ce2 annotation tracks were generated by UCSC and
collaborators worldwide.
We'd like to thank the
Genome Sequencing Center
at Washington University in St. Louis and the
Sanger Institute
for their collaborative work in sequencing the
C. elegans genome. Many thanks to the
WormBase consortium for making the worm
sequence publicly available. We'd also like to acknowledge
the UCSC team who contributed to this release: Rachel Harte
(lead engineer), Hiram Clawson (WABA and miRNA annotations),
Mike Chalup (QA), Galt Barber (QA), Heather Trumbower (QA),
and Donna Karolchik (documentation).
Posted on 22 Apr. 2004 - Mouse Genome Assembly Added to Proteome Browser
Proteome Browser functionality is now available on the
Oct. 2003 mouse genome assembly (mm4). Protein
information may be viewed for most genes in the Known Genes
track by clicking the Proteome Browser link on the gene's
details page.
For more information on the UCSC Proteome Browser, see the
news release dated 10 March 2004.
In conjunction with this release, the Known Genes and Gene
Family Browser protein data have been updated to the
Swiss-Prot version dated 15 March 2004.
Posted on 16 Apr. 2004 - Genome Browser Training - Silicon Valley Area
The UCSC Bioinformatics Group announces a seminar and
hands-on workshop on the UCSC Genome Browser, presented by
OpenHelix,
a bioinformatics training,
software testing and consulting company.
This introductory session is geared towards industry and
academic biologists engaged in genomics research. No
programming experience is required. The seminar will cover
the topics necessary
to learn how to effectively use the browser tool set,
including basic Genome Browser functionality, searching and
BLAT use, Table Browser use, creating and using Custom Tracks,
and an introduction to the Family Browser. The lecture will
be accompanied by hands-on computer exercises conducted directly on the Genome Browser web site.
The three-hour course will be held at the UCSC
Extension Campus computer lab in Cupertino, CA on Thursday,
May 6th 6-9 p.m. For pricing information or to reserve a
seat in the class, visit the
OpenHelix web site or call 1-888-861-5051.
Pre-registration is required. Academic, student, and early
registration discounts are available.
Posted on 12 Apr. 2004 - GNF Gene Expression Atlas 2 Data Now Available
Expression data from the GNF Gene Expression Atlas 2 are now
available on the July 2003 human genome assembly on the UCSC
web site. The data may be viewed graphically in the
Family Browser or via
the GNF Atlas 2 track in the Genome Browser. The track data
contain 2 replicates each of 61 mouse tissues and 79 human
tissues run over Affymetrix microarrays.
We'd like to thank the Genomics Institute of the Novartis
Research Foundation (GNF) for providing the expression data
underlying the browser displays. More information on the data
will be available in the paper Su et al. "A gene
atlas of the mouse and human protein-encoding transcriptomes"
(in press - PNAS).
Posted on 10 Mar. 2004 - Announcing the UCSC Proteome Browser
We are proud to announce a new addition to the
UCSC family of genome browsing and analysis tools. The UCSC Proteome
Browser presents a rich set of useful protein properties as well as
links to several protein and genomic data sources
on the Web. For the first time, Genome Browser users can have
both the genome and proteome worlds at their fingertips
simultaneously. The browser is accessible from the Genome
Browser via the "Proteome
Browser" link on the details page of any gene in the
Known Genes track. The initial release is available only on
Human Build 34 (hg16); Proteome Browsers for the latest mouse
and rat assemblies will follow.
For each protein, the browser displays the corresponding
genomic exon structure and its amino acid sequence.
Several protein property tracks are aligned to the sequence
to help a user pinpoint regions of interest.
Additional properties are plotted with histograms against
genome-wide protein data to
highlight significant trends and anomalies.
The Proteome Browser is tightly coupled with the UCSC Genome
Browser and UCSC Gene Family Browser, allowing easy navigation
among the tools. For example, clicking on an exon in the
Proteome Browser tracks display brings up the Genome Browser tracks
page showing
the genomic region of the exon together with a wealth of
relevant data. Similarly, clicking on the Proteome Browser's
"Family Browser" link
displays related gene family information.
The v1.0 release of the browser offers a variety of
data tracks, including amino acid and DNA sequence, exon
boundaries, hydrophobicity, polarity, cysteine and predicted
glycosylation sites, Superfamily/SCOP domains, and amino acid
anomalies. In addition, the browser includes histograms of
several properties on a genome-wide scale: pI, molecular
weight, exon count, number of cysteines, InterPro domain
counts, hydrophobicity, amino acid frequencies and anomalies.
The Proteome Browser also provides links to a variety of
external sites containing supplementary information on the protein,
including SwissProt, InterPro and
Pfam domains, 3-D structures at PDB and UCSF ModBase, and
pathway maps of KEGG, BioCarta (CGAP), and BioCyc.
We'd like to thank SwissProt for sharing their high quality
protein data and the pI calculation algorithm, as well as the other
external data sites linked to by the Proteome Browser.
We'd also like to acknowledge the hard work of Fan Hsu, lead
engineer on the project, and Jim Kent, Tom Pringle,
Donna Karolchik, and Robert Kuhn. The project received
technical input, review and support from several other members of
the UCSC Bioinformatics group.
Posted on 1 Mar. 2004 - Chicken Draft Genome Added to Genome Browser
We've added the chicken genome to the collection of assemblies available
in the UCSC Genome Browser and Blat Server.
The Feb. 2004 assembly (UCSC version galGal2) was produced by
the Genome Sequencing Center at the Washington University
School of Medicine in St. Louis. The source of
this sequence was a female inbred Red Jungle Fowl (Gallus
gallus), the ancestor of domestic chickens. The chicken
genome is the first of the avian genomes to be sequenced.
The genome has been sequenced
to 6.63X coverage. Approximately 88% of the sequence has been
anchored to chromosomes, which include autosomes 1-24, 26-28,
and 32, and sex chromosomes W and Z. (In contrast to mammals,
the female chicken is heterogametic (ZW) and the male is
homogametic (ZZ).) The remaining unanchored
contigs have been concatenated into the virtual chromosome
"chrUn", separated by gaps of 10,000 bp. The
chicken mitochondrial sequence is also available as the
virtual chromosome "chrM".
Washington University School of Medicine in St. Louis
created the physical map for this release. Genetic
mapping and linkage analysis were produced through a
collaborative effort led by Martien Groenen at Wageningen
University in the Netherlands.
SNP data based on three strains of domestic
chickens will soon be available in GenBank from an
international team of scientists led by the Beijing Genomics
Institute in China and supported by the Wellcome Trust in
Britain.
The chicken is considered to be the premier non-mammalian
vertebrate model organism. It plays an important role in
the research of viruses and cancer, and is a primary
model for the study of embryology and development. From an
evolutionary standpoint, the chicken's position
provides a good intermediate data point between mouse and
fugu. Comparative genomics analyses between the chicken and
other sequenced organisms should yield valuable
information on the evolution of gene order and
arrangement, thus improving our understanding of the
structure and function of genes.
To facilitate comparative genomics studies,
alignments of the chicken sequence to the human genome
will be available in the Genome Browser later this week.
Downloads of the comparative data are currently
available through the Downloads page (see below).
For more information about the release of the chicken genome
assembly, see the NHGRI
press release.
Additional background on the rationale behind the chicken genome
sequencing effort can be found in the
sequencing proposal.
We'd like to thank the Genome Sequencing Center at the Washington University
School of Medicine in St. Louis, Wageningen University, and
the Chicken Mapping Consortium for providing these data.
The chicken browser annotation tracks were generated by UCSC and
collaborators worldwide. See the
Credits
page for a detailed list of acknowledgements. The UCSC Chicken Genome Browser
was produced by Angie Hinrichs, Heather Trumbower, Rachel Harte, and Donna
Karolchik.
Posted on 23 Feb. 2004 - Chimpanzee Genome Browser Released
We are happy to announce the release of a Genome Browser and Blat server for the
chimpanzee (Pan troglodytes).
The 13 Nov. 2003 Arachne assembly -- labeled Chimp Build 1
Version 1 (UCSC version panTro1) -- was produced by the
Chimpanzee Genome Sequencing
Consortium.
This assembly covers
about 95 percent of the genome and is based on 4X sequence coverage.
It is composed of 361,782 contigs with an N50 length of 15.7 kb, and 37,849 supercontigs having an N50 length of 8.6 Mb (not including
gaps). The total contig length is 2.73 Gb, spanning 3.02 Gb.
The DNA donor for this genome assembly, "Clint",
is a captive-born West African chimpanzee (Pan troglodytes
verus).
Background information on the chimp genome
sequencing project and the initial news release about the chimp
assembly can be found on the NHGRI website.
Research has indicated that
the human and chimp genomes probably differ by approximately one
percent.
Because of this close relationship between chimpanzees and
humans, the assembly should facilitate comparative analyses
of the two genomes that have not been possible with other species that have been sequenced to date.
The initial release of the Chimp Browser provides several
annotation tracks comparing the chimp and human genomes.
More comparative annotations will be added in upcoming
weeks.
Bulk downloads of the chimp sequence and annotations may be obtained from the Genome
Browser FTP server or
Downloads page.
The complete set of sequence reads is available at the
NCBI trace archive.
Blat searches on chrUn_random are not supported in the initial
release, but will be available soon.
We'd like to thank NHGRI, the Eli & Edythe L. Broad Institute at
MIT/Harvard, and Washington University at St. Louis School of
Medicine for providing this sequence, and LaDeana Hillier,
Washington University School of Medicine, and the
Broad Institute for their work on the alignments. The chimpanzee
browser annotation tracks were generated by UCSC and collaborators
worldwide.
The UCSC team who worked on this release consisted of
Kate Rosenbloom, Jim Kent, Hiram Clawson, Heather Trumbower, Robert
Kuhn, Donna Karolchik, and the Genome Browser sysadmin team.
Posted on 12 Feb. 2004 - New UCSC-Supported Mirror Site
The Genome Browser project now has a UCSC-supported mirror site
that may be used during power or network outages on the UCSC
campus. The mirror
is located at the Medical College of Wisconsin in Milwaukee.
The site will be updated regularly by UCSC with the latest data and
software to closely replicate the main Genome Browser site at
http://genome.ucsc.edu.
Please continue to use the UCSC-based
site for routine Genome Browser and Blat access.
We'd like to thank the Department of Physiology at the Medical
College of Wisconsin -- and in particular Jeff Nie and Greg
McQuestion -- for their resources and collaboration on this
project.
We'd also like to acknowledge the hard work of UCSC's Paul
Tatarsky, who invested many hours in arranging the collaboration
and setting up the mirror.
Posted on 16 Jan. 2004 - Eight hg16 Tables Updated
We've discovered a handful of hg16 chrN_random_gap
and chrN_random_gold tables on our public server that are
out of date. We have replaced the following tables with
updated versions:
chr4_random_gap
chr4_random_gold
chr8_random_gap
chr8_random_gold
chrX_random_gap
chrX_random_gold
chrUn_random_gap
chrUn_random_gold
Many thanks to Grigoriy Kryukov for discovering this
problem. We apologize for any inconvenience this may have
caused to our users.
Posted on 14 Jan. 2004 - Yeast Genome Browser Released
We are proud to add yeast
(S. cerevisiae) to our growing list
of genome assemblies. The study of brewer's yeast, the most
basic eukaryotic model system, has led to important discoveries
in a wide variety of areas, including metabolism, centromeres,
recombination, cell division control, meiosis and splicing.
The S288C strain was used in this sequencing project. Reference information for
each chromosome may be found in the SGD
Systematic
Sequencing Table. For more information about the yeast genetic and physical
maps, see the paper Cherry JM et al.
Genetic and physical maps of Saccharomyces cerevisiae.
Nature 1997 387(6632 Suppl):67-73.
Downloads of the yeast data and annotations may be obtained from the UCSC Genome
Browser FTP server or
Downloads page.
We'd like to thank Stanford University, the SGD, the University of California
San Francisco (UCSF), Washington University in St. Louis, and the Eli & Edythe
L. Broad Institute at MIT/Harvard for providing the data and annotations for
this assembly. We'd also like to acknowledge the UCSC team who worked on this
release: Jim Kent, Heather Trumbower, Robert Kuhn, Donna Karolchik, and our
sysadmin team.
Posted on 10 Dec. 2003 - UCSC Releases Alignments of the Chimp Draft Assembly to Human Genome
UCSC has released alignments of the Nov. 2003
chimpanzee
draft assembly to the July 2003 human
assembly in the Genome Browser. These alignments may be
viewed on the
Human July 2003
assembly. This release coincides with today's
announcement
by the National Human Genome Research Institute (NHGRI) of the
first draft assembly of the chimpanzee genome.
The set of human/chimpanzee alignments consists of a
reciprocal best-in-genome net track and a
chimp chain track.
These alignments were generated using
the blastz program developed at Pennsylvania State
University and the programs blat, axtChain, chainNet, and netSyntenic
developed at UCSC by Jim Kent.
Research scientists should find these tracks useful for locating
orthologous regions and studying genome rearrangement in the
two species.
For more information about the alignment tracks, refer to
the track description pages. The tables may be downloaded from the
Genome Browser FTP server's
hg16 database
directory. The chimp sequence and alignment data are downloadable
from the
hg16 human/chimp
alignments directory.
The chimp sequence used in these alignments was obtained
from the 13 Nov. 2003 Arachne assembly. We'd like to thank
NHGRI, the Eli & Edythe L. Broad Institute at MIT/Harvard,
and Washington University School of Medicine for providing
this sequence, and LaDeana Hillier, Washington University School
of Medicine, and the Whitehead Institute for their work on the
alignments. We'd also like to acknowledge the members
of the UCSC team who contributed to the release of these
alignments in the Genome Browser: Jim Kent, Kate Rosenbloom,
Heather Trumbower, and Donna Karolchik.
Posted on 24 Nov. 2003 - Genome Browser Released for Mouse Assembly NCBI Build 32
We have released a Genome Browser and Blat server for the
latest mouse genome assembly, NCBI Build 32
(UCSC v. mm4). Build 32 is a composite
assembly in which chromosomes were assembled by two
slightly different algorithms depending on the available
mapping data. Chromosomes 2, 4, 5, 7, 11, 15, 18, 19, X,
and Y were assembled using a clone-based tiling path file
(TPF) provided by the Mouse Genome Sequencing Consortium
(MGSC), with whole genome shotgun sequence used to fill gaps
when necessary. The remaining chromosomes were assembled
using the MGSCv3 whole genome shotgun assembly as the TPF
and merging High Throughput Genomic Sequence (HTGS) as
needed. The UCSC mm4 assembly contains only the reference
strain C57BL/6J.
Build 32 includes 2.6 gigabases of sequence, 1.2 Gb of which is finished. We
estimate that 90-96 percent of the mouse genome is present
in the assembly. For more information about this version,
see the NCBI
assembly
notes and
Build 32 statistics.
The mm4 sequence and annotation data may be downloaded from
the UCSC Genome Browser
downloads server.
We'd like to thank the Deanna Church, Richa Agrawala, and
the Mouse Genome Sequencing Consortium
for this assembly. We'd also like to
acknowledge the work of the UCSC mm4 team: Hiram Clawson
(lead),
Terry Furey, Kate Rosenbloom, Heather Trumbower, Bob Kuhn
and Donna Karolchik, and our systems administrators Patrick
Gavin, Jorge Garcia and Paul Tatarsky.
Posted on 31 Oct. 2003 - D. melanogaster Assembly Added to Genome Browser
We have added the Drosophila melanogaster (fruitfly)
assembly to the growing collection of genomes available in
the UCSC Genome Browser and Blat servers. Release 3.1
(Jan. 2003) of the Drosophila annotated genome
sequence was provided by the
Berkeley
Drosophila Genome Project (BDGP). The 116.8 Mb euchromatic
sequence - which is virtually gap-free and of high accuracy -
contains six euchromatic chromosome arms represented by 13
scaffolds with a total of 37 sequence gaps. The sequence quality
of this release has an estimated error rate of less than one
in 100,000 base pairs in the unique portion of the sequence,
and less than one in 10,000 base pairs in the repetitive portion.
The Release 3.1 sequence was reannotated using the
Apollo
Genome Annotation and Curation Tool. We also provide data
comparing the genome of D. melanogaster with that of
D. pseudoobscura.
The fruitfly, one of the first organisms to be used in systematic
scientific investigations, has been the subject of intensive study
in genetics for nearly a century and remains a major model organism
in biomedical research, population biology and evolution.
We are pleased to add the fruitfly to the roster of assemblies
available on our site.
Downloads of the Drosophila data and annotations may be
obtained from the UCSC Genome Browser
ftp site.
We'd like to thank BDGP and the
Flybase Consortium
(Harvard University,
University of Cambridge,
Indiana University,
the University of
California, Berkeley and the European Bioinformatics Institute (EBI))
for providing the sequence, assembly, and analysis of this
genome. We'd also like to acknowledge the members of the
UCSC Genome Bioinformatics group who contributed to this
release: Angie Hinrichs (lead engineer), Heather Trumbower,
Robert Kuhn, Donna Karolchik, and Jim Kent and the system
administrators Jorge Garcia, Patrick Gavin and Paul Tatarsky.
Posted on 17 Oct. 2003 - mRNA, RefSeq and EST Data Now Updated Incrementally for Several Assemblies
Daily and weekly incremental updates of mRNA, RefSeq,
and EST data are now in place for several of the UCSC Genome
Browser assemblies. Data sets that are updated incrementally
from GenBank include the latest human (hg16), mouse (mm3),
rat (rn3), and Fugu (fr1). Others will soon be added to the
list.
Previously, these tables were updated only when we loaded a
new genome assembly into the Genome Browser or made a major
revision to a table. By updating the data on a nightly basis,
we are able to provide researchers with the most current
versions available in GenBank. All new genome assemblies
released after this date will incorporate the incremental
update technology.
Data are updated on the following schedule:
- native and xeno mRNA and refSeq tracks - updated daily at
4:30 p.m. Pacific Time (weekdays), early Saturday morning
(weekends)
- EST data - updated once per week on Saturday morning
- downloadable data files - updated weekly on Sunday morning
- outdated sequences - removed once per quarter
Mirror sites are not required to migrate to an incremental
update process, and should not experience problems as a
result of this upgrade. Mirror site questions should be
addressed to
genome-mirror@soe.ucsc.edu.
We'd like to acknowledge the hard work of Mark Diekhans in the
implementation of this new feature, and thank the QA and
sysadmin teams (particularly Paul Tatarsky) for their
support in this release.
Posted on 17 Oct. 2003 - UCSC Table Browser Enhancements
The UCSC Table
Browser is an excellent tool for retrieving and searching
the data underlying the Genome Browser. We've recently added
some new features to the Table Browser to make it even
easier to query and download data.
Many of our users have requested a batch query utility that
will allow them to paste in or upload a list of terms on
which to search. You can now do this by clicking the "Item
name/accession" button, then uploading a list of search
terms by selecting the "Paste in" or "Upload" option. Note
that the Paste option supports wildcards, but the Upload
option does not.
We've also added 2 new lists of searchable tables/tracks.
The Browser tracks list contains the names of annotation
tracks in the currently selected assembly as they appear in
the Genome Browser. This list is useful if you don't know
the name of the underlying database table that contains the
data in which you're interested. The Custom tracks list
contains the names of all custom annotation tables currently
loaded into the Genome Browser for the given assembly. This
includes tracks that have been created/loaded by the user as
well as custom annotations created via the Table Browser.
If you have feedback or questions about the Table
Browser, please send us email at
genome@soe.ucsc.edu.
Posted on 29 Sep. 2003 - Introducing the UCSC Gene Family Browser
We are pleased to announce the release of the
UCSC
Gene
Family Browser. This major new addition to our website is
a useful tool for collecting information on groups of genes
that may be related in many different ways. The
Browser provides information on gene expression,
protein homology (both within and across species), GO terms,
and Pfam domains, and cross links to many other databases.
To access the Family Browser, click the link on the top
menu on this page. The first time you use the Browser, the
application will display a brief overview of the tool and
information for starting and configuring it. To read a more
detailed description of the Browser, see the Family Browser
User's
Guide.
We are always interested in hearing feedback
about the tools on our site. If you have comments or questions
about the Family Browser, please email us at
genome@soe.ucsc.edu.
Posted on 23 Sep. 2003 - Fugu Genome Added to Genome Browser
We have added the Takifugu rubripes (Japanese pufferfish) assembly to
the growing collection of genomes available in the UCSC Genome Browser
and Blat servers. The Fugu v.3.0
(Aug. 2002) whole genome shotgun assembly --
which is the fourth
vertebrate assembly to be added to the UCSC Genome Browser -- was
provided by
the US
DOE Joint Genome Institute (JGI) as part of the
International Fugu Genome Consortium led by JGI and the
Singapore Institute of Molecular and Cell Biology (IMCB).
This assembly was
constructed with the JGI assembler, JAZZ, from paired end
sequencing reads produced by JGI and IMCB, at JGI, Myriad Genetics, and
Celera Genomics, resulting in a sequence coverage of 5.7X.
All reads are plasmid, cosmid, or BAC end sequences, with
the predominant coverage derived from 2 Kb insert plasmids.
This assembly contains 20,379 scaffolds totaling 319 million
base pairs. The largest 679 scaffolds total 160 million base
pairs. The Fugu genome was annotated using the Ensembl
system by the Fugu informatics group at IMCB.
The Fugu, which was one of the first
vertebrate genomes to be draft-sequenced after human,
serves an important role in the exploration of the human
genome. In contrast
to other vertebrates that have been sequenced, the intergenic
and intron regions of the Fugu are highly compressed and
uncluttered with repetitive sequence, resulting in a
genome that is unusually compact in size. The Fugu genome
has proved useful in gene discovery and the identification and
characterization of gene regulatory elements in other genomes.
Bulk downloads of the Fugu sequence and annotation data are
available via FTP at
ftp://hgdownload.cse.ucsc.edu/goldenPath/fr1
or through the Downloads link on the Genome Browser home page. We recommend that FTP be used rather than
HTML for the download of large or multiple files.
We'd like to thank JGI and the other members of the
International Fugu Genome Consortium, including IMCB,
the UK Human Genome Mapping Project (Hinxton),
the Molecular Sciences Institute (Berkeley) and the
Institute for Systems Biology (Seattle),
for providing the sequence, assembly, and analysis of this
genome. We'd also like to acknowledge the members of the
UCSC Genome Bioinformatics group who contributed to this
release: Kate Rosenbloom (lead engineer), Heather Trumbower,
Robert Kuhn, Donna Karolchik, and Jim Kent.
Posted on 13 Aug. 2003 - NISC Comparative Sequencing Program Regions Released in Genome Browser
The UCSC Genome Bioinformatics group has released a browser
and blat server on the first of more than 100 targeted
genomic regions being sequenced in multiple species and
analyzed by the NIH Intramural Sequencing Center (NISC)
Comparative Sequencing Program sponsored by NHGRI. This
release coincides with the publication of the results of the
study in the 14 Aug 2003 issue of
Nature
(Thomas,
J.W. et. al. (2003) Comparative analyses of multi-species
sequences from targeted genomic regions. Nature 424:788- 793).
The browser displays sequence and annotations on a large
region
containing 10 previously identified genes - including the
gene mutated in cystic fibrosis - in 13 vertebrate species.
Organisms in the study include human, chimpanzee,
baboon, cat, dog, cow, pig, rat, mouse, chicken, zebrafish
and two species of pufferfish (Fugu and Tetraodon).
The NISC Comparative Sequencing Program data may be accessed
by clicking the Browser link on the Genome Browser home page
and then selecting the "Zoo" option from the genome list.
The research team, led by NHGRI Scientific Director Eric
D. Green, included scientists from Pennsylvania State
University, University of California Santa Cruz (UCSC),
and the University of Washington in Seattle. In the study,
the investigators systematically compared the patterns of
transposon insertions among the species' sequences. One
key result of the analysis was the confirmation of recently
proposed mammalian evolutionary
trees suggesting that primates are more closely related to
rodents than to carnivores or artiodactyls. Another
significant outcome was the discovery of a
substantial number of previously unidentified non-coding DNA
segments that are conserved across a wide range of species.
Many of these regions could be identified only through
comparisons of sequence from multiple species, demonstrating
the importance of studying the genomes of a wide range of
organisms as a means for identifying functional elements in
the human genome.
UCSC built a customized version of the browser to display the
target region for this study, allowing scientists to
interactively explore the data and predictions generated
by this project, contribute data of their own, and track
the project as data from additional species are generated.
In addition to the browser, the UCSC team also
contributed to the analytical portion of the
study. Mathieu Blanchette
identified the regions that are most highly conserved among
species. Adam Siepel performed the phylogenetic analysis of
rates of substitution. The UCSC team worked with Arian Smit
to obtain definitive evidence that rodents branched off from
the common ancestor later than carnivores and artiodactyls.
For more information on the NISC study, see the Science
Dailypress release.
Flat files of the assembled sequence and annotations may be
obtained from http://www.nisc.nih.gov/data/ or via the
Downloads link on the Genome
Browser home page.
We'd like to thank the NISC Comparative Sequencing Program
team for providing the data and comparative analysis
for this Genome Browser release. Special thanks go to
Elliott Margulies at NHGRI for serving as the main liaison
between NHGRI and UCSC, and for contributing several
annotation tracks to the browser. We'd also like to
acknowledge
the efforts of the many faculty, grad students, and staff
members of the UCSC Genome Bioinformatics group who
contributed to the research effort and browser
development for this project.
Posted on 8 Aug. 2003 - New Human Genome Reference Sequence Now Available in Genome Browser
The latest human genome reference sequence (NCBI Build 34,
July 2003) is now available as database hg16 in the UCSC
Genome Browser and blat server.
There are
2,843,433,602 finished sequenced bases in the ordered and
oriented portion of the assembly, which is an increase of
0.4 percent, or approximately 11 Mb, over the Build 33
assembly.
Of particular note in this release is the addition of the
pseudoautosomal regions of the Y chromosome. This sequence
was taken from the corresponding regions in the X chromosome
and is an exact duplication of that sequence.
Some sequence joins between adjacent clones in this assembly
could not be computationally
validated because the clones originated from different
haplotypes and contained polymorphisms in the overlapping
sequence, or the overlap was too small to be to be reliable.
In these instances, the sequencing center responsible for
the particular chromosome has provided data to support
the join in the form of an electronic certificate. The
Build 34 certificates may be reviewed
here.
Bulk downloads of the data are available via FTP at
ftp://hgdownload.cse.ucsc.edu/goldenPath/hg16
or through the Downloads
link. We recommend that FTP be used rather
than HTML for the download of large or multiple files.
We'd like to thank NCBI and the International Human Genome
Sequencing Consortium for
furnishing the data, and the UCSC team members who
contributed to this release: Terry Furey, Hiram Clawson,
Heather Trumbower, Mark Diekhans, Robert Baertsch,
Donna Karolchik, Jim Kent and our sysadmin team Patrick
Gavin, Jorge Garcia, and Paul Tatarsky.
Posted on 14 Jul. 2003 - Rat Genome v.3.1 Added to Genome Browser
The UCSC Genome Bioinformatics Group has released a browser
and BLAT server on the v. 3.1 rat genome assembly from the
Rat Genome Sequencing Consortium. This
assembly (UCSC version rn3, June 2003) was produced by the
Atlas group at Baylor Human Genome Sequencing Center (HGSC).
This assembly is a minor update to the 3.0 release.
Sequence changes affect only chromosomes 7 and X. No
additional assembly releases are planned prior to the
publication of the rat genome analysis papers.
The 3.x assemblies reflect several sequence additions and
software improvements over the previous 2.x assemblies,
including the sequencing of over 1100 new BACs to cover gaps,
an improved marker set from the Medical College of Wisconsin,
a new FPC map from the BC Genome Sciences Centre, and
improved linking of bactigs. For detailed information and
statistics about the 3.x assemblies, see the Baylor HGSC
README.
We'd like to thank the Rat Genome Sequencing Consortium and
Baylor HGSC for providing this assembly, collaborators
from other institutions who have contributed annotations,
and Arian Smit for updating RepeatMasker for this release.
We'd also like
to acknowledge the contributions of several individuals at
UCSC, including Hiram Clawson, Heather Trumbower, Robert Kuhn,
Yontao Lu, Terry Furey, Mark Diekhans, Robert Baertsch,
Donna Karolchik, Jim Kent, and our sysadmin team Jorge
Garcia, Patrick Gavin, and Paul Tatarsky.
Posted on 24 Jun. 2003 - Genome Browsers Released for C. elegans and C. briggsae
UCSC has just released browsers and blat servers for 2 worms:
C. elegans version WS100 (May 2003) and C. briggsae version
cb25.agp8 (July 2002). The browsers are based on sequence
obtained from WormBase.
We are pleased to add the nematodes to the roster of genomes
available on our site. C. elegans is a major model organism
used for biomedical research, and is the first multicellular
animal to have a fully sequenced genome. In contrast, the
whole genome shotgun assembly of the C. briggsae genome is
estimated to have achieved 98% coverage. Draft chromosome
sequences are not available for C. briggsae, due to the lack
of dense chromosomal maps that allow assignment of
ultracontigs to chromosomal locations. As a result, all data
in the C. briggsae browser maps to chrUn.
Both worms played a significant role in the early history
of the UCSC Genome Browser. The browser code originated with
a C script that displayed a splicing diagram for a gene
prediction from C. elegans. Tracks for mRNA alignments and
for homology with C. briggsae were added, and the tool
morphed into the precursor of the Genome Browser, the
"Intronerator" (Kent, WJ and Zahler, AM (2000).
The intronerator: Exploring introns and alternative splicing
in C. elegans. Nucleic Acids Res. 28: 91-93).
We'd like to thank the
Genome Sequencing Center
at Washington University in St. Louis and the
Sanger Institute
for their collaborative work in sequencing the C. elegans
and C. briggsae genomes. Many thanks to the
WormBase consortium
for making the worm sequence publicly available.
We'd also like to acknowledge several UCSC people who
contributed to this release: Hiram Clawson (browser and
annotation tracks engineering), Jim Kent (WABA and
chaining/netting), Al Zahler (WABA), Heather Trumbower (QA
and project management), and Donna Karolchik (project
management and documentation).
Posted on 23 Jun. 2003 - Genome Browser UI Changes
You may notice that we've removed the Genome pulldown menu
and genome assembly information from our home page.
Genome-specific information and links, as well as genome
selection, are now available on the gateway pages for our
tools. To open up a gateway page, simply click the Browser,
Blat, or Tables link in the left sidebar.
Posted on 23 May 2003 - SARS Coronavirus TOR2 Draft Assembly Available
[NOTE: The SARS assembly is no longer available on our public site, but
may be accessed on our test server,
genome-test.cse.ucsc.edu.]
Today we'd like to announce the release of a genome browser and BLAT
server for the SARS coronavirus TOR2 draft assembly. The browser - which is based on
sequence deposited into GenBank as of 14 April 2003 - provides seven
annotations showing gene predictions, locations of putative proteins, and
viral mRNA and protein alignments. Of particular note are the protein
structure analysis and predictions, determined by using the
Sequence Alignment and Modeling (SAM) T02 tool.
This browser marks a departure from our usual collection of vertebrate
genomes. Its inception was inspired by one of our engineers - Angie
Hinrichs - who was vacationing in New Zealand when the SARs draft assembly
was initially released. Struck by the impact of SARS in that part of the
world, she downloaded the sequence and built the initial tracks from a
terminal at an Internet cafe! The rest of the team joined in on the
grassroots effort, generating the additional annotations and SAM
T02 protein analyses and predictions. Victor Solovyev chimed in with
Fgenesv+ gene predictions from Softberry Inc. UCSC does not intend to
provide a comprehensive collection of viral genomes in the future, but
will maintain this browser as long as scientific and public interest in
SARS persists.
We'd like to thank everyone who worked on this release, including
Angie Hinrichs, Robert Baertsch, Fan Hsu, Matt Schwartz, Heather Trumbower, Jim
Kent, Kevin Karplus, Donna Karolchik, Brian Raney, Hiram Clawson, Kate
Rosenbloom, Victor Solovyev, and
our extremely dedicated systems administrators Paul Tatarsky, Patrick
Gavin, and Jorge Garcia.
Posted on 21 Apr. 2003 - Chromosome 8 Data Corrected for April 2003 Human Assembly
The file that we originally used to build the agp files for the
April 2003 human release (Build 33) erroneously contained 2 contigs on
chromosome 8 that were listed twice: NT_078037, NT_008183. We've
received a corrected version and have updated the following files on our
website: contigAgp.zip, chromAgp.zip, liftAll.zip. You can obtain the
newer versions of these files from our ftp site at
ftp://hgdownload.cse.ucsc.edu/goldenPath/10april2003/bigZips/.
Posted on 14 Apr. 2003 - Human Genome Project Successfully Completed!
The International Human Genome Sequencing Consortium today announced the
successful completion of the Human Genome Project. The most
significant outcome of this project is the reference sequence of
the human genome. The sequencing of
the 3 billion letters of DNA in the human genome - which many consider to
be one of the most ambitious scientific undertakings in history - was
completed 2 years ahead of schedule and at substantially less cost than
original estimates. The reference sequence will serve as a new foundation
for research in the fields of medicine and human biology.
In conjunction with this announcement, the UCSC Genome Bioinformatics
group is proud to release a genome browser and BLAT server on the
reference sequence (NCBI Build 33), along with bulk downloads of the
sequence and annotation data. The initial browser provides a preliminary
set of annotations that will be expanded in coming weeks. Bulk downloads
of the data are available via FTP at
ftp://hgdownload.cse.ucsc.edu/goldenPath/10april2003
or through the Downloads link on this page.
We
recommend that FTP be used rather than HTML for the download
of large or multiple files.
The reference sequence covers about 99 percent of the human genome's gene-containing
regions, and has been sequenced to an accuracy of 99.99 percent. The
missing portions are essentially contained in less than 400 defined gaps
that represent DNA regions with unusual structures that can't be reliably
sequenced using current technology. The average DNA letter now lies within
a stretch of approximately 27,332,000 base pairs of uninterrupted
sequence!
Chromosomal sequences for this release were assembled by the
International Human Genome Sequencing Consortium sequencing centers and verified by
NCBI and UCSC. In some cases, sequence joins between adjacent clones
could not be computationally validated, e.g. due to polymorphisms in the
overlapping sequence. In situations like this, supporting evidence for
the join has been provided by the sequencing center responsible for that
particular chromosome. The
Non-standard Join Certificates table displays this information. The
annotations on the UCSC website have been provided
by UCSC and collaborators worldwide. See the
Credits page for a detailed
list of organizations and individuals who contributed to the success of
this release.
We'd like to congratulate the many people worldwide who have worked on
the Human Genome Project for this landmark achievement. We'd also like to acknowledge the UCSC
Genome Browser project team who worked many long hours to ensure that
the genome browser and sequence data were released on time for this
announcement: David Haussler, Jim Kent, Terry Furey, Matt Schwartz, Heather Trumbower,
Angie Hinrichs, Fan Hsu,
Donna Karolchik, Jorge Garcia, Patrick Gavin, Chuck Sugnet, Yontao Lu, Mark Diekhans, Ryan Weber, Robert Baertsch, Krishna Roskin, and the many other students in the UCSC Genome Bioinformatics group.
Posted on 2 Apr. 2003 - Human Assembly hg10 and Mouse Assembly mm1 Archived
The Dec. 2001 Human assembly (hg10) and the Nov. 2001 Mouse assembly
(mm1) have been moved to the archives. They are no longer viewable in the main browser, but
can still be downloaded from the
downloads server.
Posted on 26 Mar. 2003 - New Rat Assembly Released in Genome Browser
We've added an updated rat assembly to our site: Rat Jan 2003 (rn2). This
corresponds to the Version 2.1 Jan 2003 Update of the rat genome
assembly, produced by the Atlas group at Baylor HGSC as part of the Rat
Genome Sequencing Consortium.
This update corrects duplications that were assembly artifacts in the
previous version and improves the linking of bactigs to create larger
"ultrabactigs". Compared with the previous rat assembly, sequence mapped
to specific chromosomal coordinates is reduced by about 1.6 percent.
Loosely mapped and unmapped sequence is reduced by 17 percent. For more
details and statistics on the Jan 2003 assembly, see the Baylor HGSC
README for this release.
UCSC has released a Genome Browser and BLAT server for this assembly
update. The initial
browser contains 16 annotation tracks, with more to follow in coming
weeks. Sequence downloads are currently available at
ftp://hgdownload.cse.ucsc.edu/goldenPath/rnJan2003/ or via the Downloads
link on this page. A complete set of database downloads will be available at the beginning
of next week. This data contains
specific
conditions for use.
Thanks to the Atlas group at Baylor HGSC, the Rat Genome Sequencing Consortium,
the UCSC Genome Bioinformatics group, and contributors worldwide for
making this release available.
Posted on 13 Mar. 2003 - Updated Mouse Genome Assembly Now Available
We're happy to announce an update to the mouse genome sequence. This new
version (Mouse Feb. 2003) includes 705 megabases of finished sequence,
compared to 96 megabases of finished sequence in the previous assembly.
Many people in the Mouse Genome Sequencing Consortium contributed to
this update. The Sanger Institute in particular contributed a large
amount of finished sequence. Richa Agarwala, Deanna Church, and
coworkers at NCBI layered the finished clones on top of the Arachne whole genome shotgun assembly. Arian Smit constructed a new RepeatMasker
library.
UCSC has released a Genome Browser and BLAT server for the Feb. 2003
Mouse genome. The initial
browser contains 14 annotation tracks, with more to follow in coming
weeks. Sequence downloads are currently available at
ftp://hgdownload.cse.ucsc.edu/goldenPath/mmFeb2003/ or via the Downloads
link on this page. Database downloads will be available at the beginning
of next week.
Thanks to everybody at UCSC and around the world that contributed to the
success of this release!
Posted on 5 Feb. 2003 - Enhanced Version of Genome Browser Released
We're proud to announce the release of version 17 of the UCSC Genome
Browser.
This version contains powerful new features, numerous improvements to
the annotation track display, additional annotation
tracks, and a number of bug fixes. In this release cycle, we've also
introduced
an enhanced QA process that formalizes our testing and verification
of the Genome Browser software and the data displayed in the browser.
New functionality in v.17:
-- Numerous enhancements to the table browser that allow the user to
conduct more complex and specific searches. New features include support
for intersections of tracks, a new summary statistics output format, and
the ability to output query results as a custom annotation track that
can be viewed in the Genome Browser.
The new
Table Browser User's Guide contains a detailed
description of the new features and provides a wealth of information and
examples for conducting various types of searches on the database tables.
-- Two new display modes available for most annotation tracks: pack and
squish modes. In pack mode display, annotation track features are f
ully
displayed, but more than one feature may be displayed on the same line.
This greatly reduces the amount of display space needed by a track
when a user wishes to view a large number of individual features at one
time. Squish mode is similar to pack mode, but displays features
at 50% height and without labels. This mode is particularly
useful for viewing tracks in which a large number of features align to
the same section of a chromosome, e.g. EST tracks.
-- Functional groupings of annotation track controls. This
makes it much easier to find a particular item in the track control list
and gives a better visual overview
of the annotations available in a particular category, e.g. comparative
genomics tracks or gene prediction tracks.
-- A mechanism for saving the annotation tracks image in postscript or
PDF format. This much requested feature enables Genome Browser users to print an image at
high resolution, edit it with a drawing program, or display it in a
postscript or PDF viewer.
-- A collection of custom annotation tracks supplied by
Genome Browser users and members of the UCSC Genome Bioinformatics lab.
Additional contributions to this collection are welcome! Contact
genome@soe.ucsc.edu
if you have an annotation you'd like to share.
New annotation tracks in v.17:
-- a new Known Genes track (Human Builds 30 & 31, Feb 2002 Mouse,
Nov 2002 Rat) that shows known
protein coding genes based on proteins from SWISS-PROT, TrEMBL, and
TrEMBL-NEW and their corresponding mRNAs from Genbank. Features within
the track are color-coded according to origin and review status.
-- a new Superfamily track (Human Build 30, Feb 2002 Mouse) that shows proteins having
homologs with known structures or functions. Each entry in the track
shows the coding region of a gene (based on Ensembl gene prediction).
The feature label consists of the names of all known protein domains coded
by the gene, and usually contains structural and/or function
descriptions that provide valuable information for getting a quick grasp
of the biological significance for the gene.
We have also released several additional annotation
tracks on the latest human and rat assemblies in the past
month.
Bug fixes in v.17:
-- Approximately 40 bugs (mostly minor problems) have been fixed in
this version.
To take full advantage of the new display features in this release, we
recommend that you reset your browser to the new default settings. NOTE:
you may not want to reset your browser if you have customized settings
that you wish to preserve. You can reset your browser by clicking
the "Click here to reset" link on the Browser Gateway page.
We hope this new release facilitates your work with the UCSC Genome Browser.
If you have any questions or comments about the new release, send email
to genome@soe.ucsc.edu.
Posted on 23 Dec. 2002 - Human Genome Assembly Build 31 Released in Genome Browser
We're pleased to announce the release of the latest human genome
assembly, Build 31 (UCSC version hg13). This assembly was produced at NCBI
based on sequence information submitted into GenBank as of Nov. 14, 2002.
Release notes for this assembly are available from the
NCBI web site. Because UCSC now obtains its assembly directly from
NCBI, the UCSC Build 31 data is identical to that of NCBI and Ensembl.
Build 31 is an excellent high-quality assembly that shows a remarkable
amount of progress toward the milestone of finishing
the human genome. Greater than 95% of the euchromatic region of the
genome is now complete, with more than 90% of the sequence in a
finished state. The number of clone contig gaps has decreased by one
third from the previous assembly, and the overall number of sequenced
contigs has been reduced by one half. Seven chromosomes are considered to
be in a finished state: 6, 7, 13, 20, 21, 22, and Y.
The initial release of the Build 31 Genome Browser contains 25 annotation
tracks, with several more to follow in the upcoming weeks. Bulk
downloads of the data are available from our FTP site at
ftp://hgdownload.cse.ucsc.edu/goldenPath/14nov2002 or via the
Downloads link on this page.
UCSC has generated a set of high-level comparisons of the Build 31
draft sequence against various types of information (STS maps, BAC end
pairs, and clone overlaps). This information, as well as statistics for
Build 31, is accessible from the
Chromosome Reports,
Genome Map Plots, and
Summary Statistics
links in the "Technical Information about the Assembled Sequence"
section below.
We'd like to thank NCBI as well as all the people who collaborated on the
data and annotations for this release.
Posted on 6 Dec. 2002 - Rat Genome Assembly Now Available in Genome Browser
We're pleased to announce the release of a UCSC Genome Browser on the
Nov. 2002 rat assembly produced by the Baylor College of Medicine Rat
Genome Sequencing Center and the Rat Genome Sequencing Consortium.
The sequence was assembled using a hybrid approach that combines the
clone by clone and whole genome shotgun methods. A new software program -
ATLAS - was developed for this effort. The assembly process resulted in
a 6.5-fold coverage of the rat genome, which is estimated to be
approximately 2.8 Gigabases in size.
Downloads of the rat data and annotations are available through our
ftp site at downloads server.
This data contains
specific conditions for use. The sequence is also
available from the
Rat
Genome Project website for the Human Genome Sequencing Center at
Baylor College of Medicine or from GenBank.
We'd like to thank the Baylor team and the Rat Genome Sequencing
Consortium for their collaboration on this project. See the
Credits page
for a complete list of acknowledgments.. For more
information on the rat genome, the assembly process, and the
Rat Genome Sequencing Consortium, refer to the website for the
Human Genome Sequencing Center at Baylor College of Medicine.
Posted on 5 Dec. 2002 - Mouse Genome Browser Released
The International Mouse Genome Sequencing Consortium has announced
the publication of a high-quality draft sequence of the mouse genome,
together with a comparative analysis of the mouse and human genomes.
The results from this analysis can be found in the Mouse Genome
Browser on this website. The paper appears in the Dec. 5 issue of the
journal Nature at
http://www.nature.com/nature/mousegenome/.
The co-author list includes several members of the UCSC Genome
Bioinformatics Group: CBSE Director David Haussler, Research
Scientist Jim Kent and research team members
Robert Baertsch, Mark Diekhans, Terrence Furey, Angie Hinrichs, Fan Hsu,
Donna Karolchik, Krishna Roskin, Matt Schwartz, Charles Sugnet and Ryan
Weber.
Posted on 29 Oct. 2002 - Additional Data Downloads Available for Human Assembly June 2002
We've added several new directories of downloadable data to the 28 June
2002 human genome assembly. These directories contain mouse/human
alignments of the June 2002 human assembly vs. the Feb. 2002 mouse assembly. You can access
these directories from our downloads server.
Within the main directory vsMm2 are 3 subdirectories that contain all
the alignments (axtAll), alignments filtered to provide only the best alignment
for any given region of the human genome (axtBest), and a relatively stringent
subset of the axtBest alignments (axtTight). For more information
about the format of the alignment files and the methods used to generate
the alignments, consult the README.txt file in the vsMm2 directory.
Posted on 18 Oct. 2002 - Enhancements in v16 Genome Browser
We've rolled out a new version of the Genome Browser - v.16. In
addition to several bug fixes, this release contains some interesting
new features.
The Table Browser has undergone major enhancements. Users
can now restrict their queries by specifying a value or range for any of
the fields in a table, and by selecting which fields should be displayed in
the output. The Table Browser also provides the ability to do a free-form SQL
query on a table and supports several new output formats.
We've extended the capabilities of the DNA retrieval functionality
in the Genome Browser and the Table Browser. The new
mechanism offers the user several options for configuring the amount and
type of sequence region that is retrieved, and options for formatting the
sequence output. The retrieval options vary based on the type of table
selected.
The Genome Browser's gene prediction tracks now offer a Comparative
Sequence link in addition to the predicted protein, mRNA sequence, and
genomic sequence links. The Comparative Sequence feature displays
annotated codons and translated protein for the region in alignment to
another species.
a logarithmic scale and displays in the track as "mountain ranges". Details
pages associated with the individual peaks in the track provide access to
the base level alignments for the whole region and for the individual 50bp
windows.
The team that produced this track includes Ryan Weber, Krishna Roskin,
Mark Diekhans, Jim Kent, Scott Schwartz, and Webb Miller.
Posted on 12 Sep. 2002 - "User's Guide to the Human Genome" Features UCSC Genome Browser
Nature Genetics has just published User's Guide to the Human Genome, a
hands-on tutorial for using genome browsers as web tools for browsing and
analyzing data from the Human Genome Project and other sequencing efforts. The
3 browsers featured in the tutorial include the UCSC Genome Browser, NCBI's
Map Viewer, and the Ensembl Genome Browser. The guide is organized around a
collection of step-by-step solutions to 13 typical research questions,
and serves as a nice supplement to the documentation materials
available on the UCSC Genome Browser web site. The guide is accessible as a
link off the Nature Genetics home page at
http://www.nature.com.ng.
Posted on 12 Sep. 2002 - Correction to Human Assembly hg12 Chromosome Bands Annotation
We've corrected a problem with the Human June 2002 (hg12) cytoBand annotation
track that affected chromosome Y. The clones on this chromosome were
erroneously pushed from the q-arm onto the p-arm, creating some confusion. The
currently available version of the cytoBand data on this website contains this
correction.
Posted on 15 Aug. 2002 - Additional Annotations for Human Draft Assembly hg12 Released
We've just released several new annotation tracks/tables for the human genome.
On the June 2002 assembly, we've added Gene Bounds,
UniGene, CpG Islands, Nonhuman mRNA & EST, SNPs, NC160, and GNF Ratio.
On the April 2002 assembly we've added a Fgenesh++ Genes track, and have also
updated the RepeatMasker track. The Dec. 2001 release now includes a Sanger 22
track.
On the mouse genome, we have 2 new tracks for the Feb. 2002 assembly:
TIGR Gene Index and RNA Genes.
Posted on 6 Aug. 2002 - Error with Six Chromosome 3 Contigs in Human Assembly hg12
We have fixed an error with six of the chr3 contigs in the bigZips/contigAgp.zip
file. The following .agp files were corrected: NT_005684.agp, NT_005663.agp,
NT_022554.agp, NT_022459.agp, NT_006031.agp, and NT_022419.agp. The
chr3.agp file in bigZips/chromAgp.zip was also modified. This change does not
affect the .gl files, the .fa files, the
lift files, or the annotations. Alignments made on the previous version
of chr3 are still good. Updated versions of the contigAgp.zip and
chromAgp.zip files were
uploaded to our site today. You can download the new versions via ftp from our
downloads server.
Posted on 2 Aug. 2002 - New RepeatMasker Track Available for Human Assembly hg12
The problems with the June 2002 Build 30 (hg12) RepeatMasker track have been
resolved. The new RepeatMasker track, along with regenerated Fish Blat
and Genscan tracks, are now available in the Browser and
through our
Downloads link. We've also added a few new annotation tracks for the
June 2002 release, and will be adding more over the next 2 weeks.
The latest Genome Browser has 2 new features. We've added filter
functionality to the Table Browser, accessible via the Filter Fields
button on the Table Browser main page. Also, some of the Dec. 2001 human genome tracks (eg. RefSeq Genes) now have a
Comparative Sequence link from the details page that shows annotated
codons and translated protein with alignment to the mouse genome.
Posted on 27 Jul. 2002 - Problems with Repeat-masking on Human Assembly hg12
We've experienced some RepeatMasker problems on Build 30 and are
rerunning it. This will directly affect the RepeatMasker track and the
masking of the fasta files. The Fish Blat and Genscan tracks may also
change slightly once we're redone this. The EST, mRNA, and RefSeq tracks
should not be affected. We will also post a new RepeatMasker track for
Build 29 (see news item below) as soon as the Build 30 tracks are
completed. We apologize for any rework this may cause.
Posted on 26 Jul. 2002 - Bulk Data Downloads Now Available for Human Assembly hg12
Bulk downloads of the June 2002 Build 30 human genome assembly (hg12) are now
available from the downloads server.
This initial release of the annotation database download contains a limited set of
tables. Additional files will be available for download next week.
Posted on 24 Jul. 2002 - Human Assembly hg12 Blat Server Available
The BLAT server and the coordinates conversion feature for human genome
assembly Build 30 (hg12) are now functional.
Posted on 23 Jul. 2002 - Pre-release of Human Draft Assembly Build 30 in Genome Browser
We're pleased to announce the pre-release of a browser for
human genome assembly Build 30 from NCBI (UCSC version hg12). This assembly was
produced at NCBI based on sequence information submitted into GenBank as of
June 28, 2002. Build 30 release notes and statistics will soon be
available from the NCBI web site.
Build 30 is an excellent high-quality assembly. It contains nearly 87%
finished sequence, and 94%-97% coverage. The sequence coverage of this build
is much higher than in previous releases, and there is a high level of
correspondence between the sequence and the map. Currently, the human genome
project appears to be on track to achieve the goal of finishing at least 95%
of the human genome (using Bermuda standards) by April 2003.
UCSC has generated a set of high-level comparisons of the Build 30 draft
sequence against various types of information (STS maps, BAC end pairs, and
clone overlaps), accessible from the
Chromosome Reports and
Genome Map Plots links in the "Technical Information about the Assembled
Sequence" section below.
A Blat server for Build 30 is not yet available, but should be
accessible from this site later this week. Data for the mitochondrial genome
and several more annotation tracks will be posted for this release as they
become available. Bulk downloads of the hg12 data should be available from
this site in a few days.
Posted on 9 Jul. 2002 - Repeat-masking Problems on Human Assembly hg11
We've found some problems with the repeat-masking of the Build 29 (hg11)
human sequence. We're in the process of replacing the RepeatMasker
track, but do not plan to redo the other tracks due to the imminent
release of Build 30. Because of this, we advise that you do not use the
cross-species tracks for statistical purposes.
Posted on 1 Jul. 2002 - New Look for UCSC Genome Bioinformatics Home Page
The UCSC Genome Bioinformatics home page is sporting an updated interface to
accommodate the growing number of organisms supported by the UCSC Genome
Browser, BLAT, and Table Browser. The list of assembly versions accessible
through each of these tools can now be found on the tool's Gateway page. To
reach the Gateway page, choose an organism from the dropdown list on the left
sidebar of this page, then click the Browser, BLAT, or Tables link. New
organisms will be added to the list in the months ahead.
The UCSC site continues to provide a variety of bulk downloads of a genome
assemblies and annotations. The list of downloadable data has been removed
from the home page, but is readily available through the Downloads link on
the left sidebar. The downloads list can also be accessed directly at
http://hgdownload.cse.ucsc.edu/downloads.html or through
our ftp site at
ftp://hgdownload.cse.ucsc.edu/goldenPath/.
Several new annotation tracks have been added to our site in the past
couple weeks. The Feb. 2002 mouse assembly now has tracks for BAC End pairs,
Fgenesh++ gene predictions, and AltGenie gene predictions based on Affymetrix's
Genie gene-finding software. New to the Apr. 2002 human assembly is the
GenMapDB Clones track, which shows placements of BAC clones from the GenMapDB
database based on BAC end sequencing information and confirmed using STS
markers by Vivian Cheung's lab at U. Penn. We've also changed the Known Genes
track name to RefSeq Genes in all assemblies.
Posted on 24 May 2002 - Bulk Data Downloads for Human Assembly hg11 Now Available
Bulk downloads of the April 2002 hg11 human genome assembly (NCBI Build 29)
are now available from the downloads server".
Posted on 22 May 2002 - Human Draft Assembly Build 29 Released in Genome Browser
We've just released a browser and BLAT server on
the latest Build 29 human genome assembly from NCBI (UCSC
version hg11). This assembly is based
on sequence information submitted into GenBank as of Apr. 5 2002. As with the
Dec. 2001 (hg10) release, this assembly was produced at
NCBI rather than at UCSC. Consult NCBI's
Build 29 release notes and
statistics for more information about this release.
This assembly contains nearly 75% finished sequence.
Currently, the human genome project appears to be on track to achieve the goal
of finishing at least 95% of the human genome (using Bermuda standards) by April 2003.
Although the NCBI human genome assembly has been steadily
improving over the past year, mapping problems still exist in
the current release. Most are small, relatively local rearrangements.
Larger scale problems include a rearrangement in the p-arm of Chr16 and
several discrepancies in Chr17. Researchers - especially positional
cloners - are strongly encouraged to use the tools provided
(comparison plots, chromosome reports) to evaluate the
accuracy of the assembly in specific regions of interest.
Bulk downloads of the hg11 data should be available from this site
in approximately one week. New annotation tracks will be posted as soon
as they become available.
Posted on 24 Apr. 2002 - Bulk Data Downloads of Mouse Assembly Feb. 2002 Available
Bulk downloads of the February 2002 mouse genome assembly are now available
from the downloads server.
Posted on 19 Apr. 2002 - New Mouse Genome Assembly Released
The February 2002 mouse genome assembly is now available in the browser and
for BLAT searching. This assembly was produced at the Whitehead Institute
using their Arachne software. We'd like to thank them and the Mouse Genome
Sequencing Consortium for providing this assembly, which has
specific conditions for use.
Bulk downloads of the data should be available in approximately one week.
Coordination with mouse genome data access at
Ensembl and
NCBI is
in progress. We'd also like to acknowledge the UCSC team that produced this
release: Jim Kent, Terry Furey, Matt Schwartz, Fan Hsu, Yontao Lu,
Donna Karolchik, Chuck Sugnet, and Ryan Weber.
Posted on 9 Apr. 2002 - Bulk Data Downloads of Mouse Assembly Nov. 2001 Available
Bulk downloads of the November 2001 mouse genome assembly are now available
from the downloads server.
Posted on 2 Apr. 2002 - Release of New Genome Browser Version and Mouse/Human Annotations
An updated version of the UCSC Genome Browser (v.11) is now available.
Along with the v.11 browser, we've released several new annotation tracks on
the latest human and mouse assemblies. The new Human Dec. 2001 tracks include:
Mouse Synteny, Ensembl, Genscan, CpG Islands, Mouse Blat, Fish Blat,
Unigene/SAGE, NCI60 Microarray, GNF Affymetrix Microarray, Rosetta
Microarray, and SNPs. An STS Markers track has been added to the Mouse
Nov. 2001 browser.
Posted on 14 Mar. 2002 - Mouse Draft Assembly Nov. 2001 Released in Genome Browser
The November 2001 mouse genome assembly is now available
for viewing in the browser and for BLAT searching. This assembly
was produced at the Sanger Center using the Phusion software developed
by Jim Mullikin and Zemin Ning, and was tied to the
mouse fingerprint map by Tim Hubbard. We'd like to
thank them and the Mouse Genome Sequencing Consortium for providing this
assembly, which has specific
conditions for use. Bulk downloads of the data
will be available in approximately one week. Coordination with
mouse genome data access at
Ensembl and
NCBI
is in progress. We'd also like to acknowledge the UCSC team that produced
this release: Jim Kent, Terry Furey, Matt Schwartz, Fan Hsu, Yontao Lu,
and Donna Karolchik.
Posted on 16 Feb. 2002 - Human Genome Assembly Build 28 Now Available
A new assembly based on sequence submitted as of Dec. 22 in Genbank (Build 28) is
now available in the browser and for BLAT search.
This assembly was produced at NCBI rather than UCSC, primarily by
Richa Agarwala, Greg Schuler, and Paul Kitts. The NCBI assembly has
been steadily improving over the past year. Currently it shows slightly
better local order and orientation compared to the UCSC assembly on the
same sequence, but somewhat worse tracking of the chromosome level maps.
The NCBI assembly has the advantage that it can be generated significantly
faster than the UCSC assembly. With the human genome sequencing now
in the end game - over two thirds of the human clones are now finished -
we feel it more productive to focus worldwide annotation efforts on a
single assembly rather than continue producing competing assemblies.
We're working with NCBI to improve their map tracking.
Posted on 4 Feb. 2002 - Chromosome Reports Released
Chromosome Reports detailing correspondence with STS map, overlap,
and BAC end sequence information are available under the "Technical
Information About the Assembled Sequence" section below. This also
gives information about the clone map on which the assembled sequence
is based.
Posted on 18 Dec. 2001 - New Genome Browser Enhancements
There are some major enhancements to the browser. The complete user interface settings
including track controls, labels, and position are now saved from session to session.
You can configure the browser once to your liking and it will stay that way. This feature
will only work if cookies are enabled in your browser. If you
want to restore the default settings use the reset all button under the main graphic.
Also under the main graphic are new controls that move just the start or just the end
of the genome window. These are useful for getting exactly the right view without having
to do arithmetic on the position. These controls by default will move two guideline units
at a time, but you can specify other increments. There's a new page associated with each
track. This page is accessible by clicking on the mini-buttons to the left of the track
in the main graphic, or by clicking on the new hyperlink associated with the track in the
track controls section under the graphic. These pages contain a description of the track
and in many cases new controls. The mRNA and EST associated controls let you color or
filter the display according to tissue, author, organism, and so forth.
As with any new enhancement there are likely to be a few new bugs too.
Many of these have been spotted and fixed already. Please let us know
if you find a problem that persists more than a day or two. It's always helpful to include
the freeze and genomic position with a problem report.
Posted on 30 Nov. 2001 - Link Added to Jackson Lab's MGI Mouse Orthologs
There is now a link from the known genes details page to the Jackson Lab's MGI Mouse Ortholog
when the ortholog is known. Thanks to Carol Bult for her help setting up this link.
Posted on 29 Nov. 2001 - Duplications Track Released for August Browser
A duplications track is now available in the August browser. This track
shows duplicate blocks of sequence larger than 1000 bases. The track is hidden
by default. To open it look for 'Duplications' in the third row of track controls
under the main graphic window, and change the setting to 'dense'. Thanks to Evan Eichler
and Jeff Bailey for this track.
Posted on 28 Nov. 2001 - Sanger Curated Gene Annotations Now Available on Chromosome 20
Sanger curated gene annotations are now available on chromosome 20. Thanks to
Jennifer Ashurst, James Gilbert, and all the annotators at the Sanger Institute.
Posted on 27 Nov. 2001 - Haplotype Blocks Annotation Released for Chromosome 21
A new track has been added to the August freeze browser showing
haplotype blocks derived from common SNPs on Chromosome 21 by Perlegen,
as described in "Common
High-Resolution Haplotypes." Patil, N. et. al. Science 294:1719-1723 (2001).
Posted on 19 Nov. 2001 - SNP and Mouse Blat Tracks Available
The SNP and Mouse Blat tracks are now available
for August. The Mouse Blat track uses a partial assembly of
the public whole genome shotgun data courtesy of Whitehead's
Arachne program.
Posted on 8 Nov. 2001 - Interface of Track Details Pages Updated
The detail web pages for each of the tracks have been updated to reflect
the overall look and design of this site. You will now see the familiar
blue navigation bar with links to the Browser, BLAT, Downloads, and the
FAQ page from each of the track detail pages.
Posted on 8 Nov. 2001 - STS Markers Track Updated on Apr. and Aug. Browsers
The STS Markers track has been updated on the April and August browsers to
now include much more information on the detail page including links to
UniSTS and details on the alignments of the markers to the draft sequence.
In addition, all known aliases of the markers can be entered in the
"position" window, and the corresponding merker will be found and
displayed if its location has been determined.
Posted on 8 Nov. 2001 - FISH Clones Track Added to Apr. and Aug. Browsers
A new FISH Clones track has been added to the April and August browsers.
Previously, this information has been included in the STS Markers track.
Now, this has been broken out into a separate track with additional
information provided on the detail page not previously shown.
Posted on 6 Nov. 2001 - Fgenesh++ Gene Predictions and Cross-Species mRNA Tracks Available
The fgenesh++ gene prediction and the cross-species
mRNA tracks are now available in the August browser.
Posted on 31 Oct. 2001 - DNA Button Functionality Upgraded
The 'DNA' button at the top of the browser has been significantly
upgraded. By default it now returns DNA that has repeating elements
in lower case and other DNA in upper case. There is also an option to
color the DNA output with various tracks. You can have the case and font
features such as underline, bold, and italic follow tracks too.
Posted on 29 Oct. 2001 - TIGR Gene Index Track Added to April Browser
There is now a TIGR Gene Index track
in the April 2001 freeze browser. The TIGR Gene Index is based
on alignments of assembled ESTs from a number of species.
Be sure to click into the track and follow the outside links to
the TIGR site, which contains a wealth of information on the genes.
Posted on 29 Oct. 2001 - Acembly Track Updated on August Browser
The Acembly track on the August 2001 freeze
has been updated to include predictions based on human ESTs
and Genbank mRNAs as well as RefSeq human mRNAs. Protein
predictions are now also available in the details page for this
track. The outside link for this track is also very informative.
Posted on 27 Oct. 2001 - Share Your Custom Annotation Tracks!
You can now share your custom tracks with the
community. The easiest way to do this is to construct a link from your own
web pages to the browser. Here is an example of a URL for
such a link:
The position variable tells the browser which part of the genome to
display. The db variable refers to the freeze number.
'hg8' corresponds to the August 2001 freeze. The customText
variable should refer to a URL containing plain text in one of the
formats described in
http://genome.ucsc.edu/goldenPath/help/customTrack.html.
Note that generally we only keep the last three versions of the
genome online (hg6, hg7, and hg8). You'll have to update
your link and track about every 4 months as a result.
Please send in the URLs of tracks you'd like to share to
genome@soe.ucsc.edu,
along with a brief description of
the track and the genome version it is tied to. We'll create
an index page of these here.
You can also access an external custom track by including
the URL of the track data (on a separate line starting with
http://) in the custom track box at the bottom of the browser gateway.
Posted on 15 Oct. 2001 - Weekly Updates of Tab-delimited Data Files
Fresh tab-delimited files from the browser database
are now available. They will now be updated automatically
every Sunday evening. The table browser queries the database
directly, so it is always up to the minute.
Posted on 12 Oct. 2001 - New Gene Prediction Tracks for Apr. and Aug. Browsers
Several new sets of gene predictions came in this week.
We now have fgenesh++ predictions for the April freeze,
and Genscan and Acembly predictions for the August freeze.
Posted on 11 Oct. 2001 - Table Browser Upgraded
Why struggle with massive genomic file downloads when the UCSC
Table Browser
lets you select exactly the track data desired via a convenient web
interface? Major new improvements by Krish Roskin have empowered and
simplified this feature available now for the three most recent assemblies.
Posted on 8 Oct. 2001 - Oct. 2000 Assembly Moved to Archives
The October 2000 assembly has been moved to the
archives
to make room for the August assembly.
Posted on 5 Oct. 2001 - Revised Aug. 2001 Assembly Released
A revised August 2001 freeze assembly is now up. The problems
with flipped contigs of finished clones and high levels of
sequence duplication are fixed. You can now download this
assembly in bulk as
well as browse it. Chromosome by chromosome and annotation
database files will be following over the next day or two.
Posted on 2 Oct. 2001 - Convert Coordinates Between Different Draft Assemblies
You can now convert coordinates between different versions of the draft
using a new program, hgCoordConv, by Chuck Sugnet.
hgCoordConv attempts to cut out sequences of the original
draft and align them to the new draft. When aligning the
sequences to the new draft hgCoordConv makes sure that the
sequences are in the same order, orientation, and have the
correct distances between them.
Chuck has also implemented a SAGE/Unigene track in the browser.
This track displays data from the
SAGEMap project at NCBI. UniGene cluster sequences are
displayed in the browser and colored according to their average SAGE
counts over a series of experiments. Selecting one of the UniGene
representative sequences displays the SAGE results for UniGene
sequences.
Posted on 21 Sep. 2001 - Clone Order Problems Found in Preliminary Aug. 2001 Assembly
Some systematic problems were found in the clone order on the
preliminary August 2001 freeze assembly. The sequencing center at
Washington University, EBI's Ensembl group, and our group here at UCSC
are currently working together to revise the merged BAC clone maps and
the assembly process to fix these problems. We hope to update the August
browser with a revised assembly soon. Then, after further testing via
the browser, we will release the assembled August freeze genome sequence
itself.
Posted on 11 Sep. 2001 - Preliminary Aug. 2001 Assembly Now Available in Genome Browser
A preliminary assembly of the August 2001 freeze is now
available in the genome browser. Due to significant progress
by the mapping and finishing groups of the international
public consortium, this assembly is a major improvement over
the April 2001 freeze assembly. Imre Vastrik, Ewan Birney and
colleagues at Ensembl have computed a merge of BAC clone maps
provided by the individual sequencing centers with
fingerprint-based maps prepared at Washington University. These
merged maps were used for the first time in this August
assembly.
The August assembly has successfully passed our internal
quality control tests. We will release the sequence and
annotations in bulk downloadable form in a week or so, after
the external testers have had a chance to further verify
it. Meanwhile if you notice any systematic problems please let
us know at
genome@soe.ucsc.edu.
Though the state of the working
draft has improved considerably, remember that where you see
solid marks in the 'gap' track, the relative order and
orientation of flanking contigs is still uncertain. In some
cases of complex repeat structure it is also possible that
the assembly may be incorrect even in the absence of gaps.
Also, sometimes ambiguities in the data cause a BAC clone to be
split, with parts of it placed at opposite ends of a run of other clones.
Localized errors of this type should be corrected by additional
finishing efforts at the individual sequencing centers and
should not be reported to UCSC. However, please report any
large-scale or systematic problems you detect with this assembly
that could have been caused by our data processing.
The tracks available on the August 2001 browser are quite
limited at the moment. More tracks will show up over time.
Posted on 11 Sep. 2001 - April 2001 Assembly is New Default in Genome Browser
The April 2001 assembly is now the default for the browser.
The SNP and Ensembl gene tracks have come in for this version.
There is also a new track depicting non-human vertebrate mRNA
alignments.
The Sept. 2000 and July 2000 versions of the genome are
now only available on our archive site. Please see the link
in the blue box to the left for more details.
The August 6 freeze is progressing through the pipeline.
We've recently received an updated accession map from Wash U.
Ensembl will shortly be integrating this with chromosome
specific maps from the sequencing centers. We are still
on track for an early September next release.
Posted on 28 Aug. 2001 - Custom Annotation Track Functionality Added
Meanwhile we've been continuing work on the genome browser.
It's now possible to upload your own annotations to be displayed
alongside the built-in tracks. Please scroll to the bottom of the
browser gateway pages for further information. The browser has
also been sped up, particularly on the larger chromosomes by
using a 'binning' technique suggested by Lincoln Stein and Richard Durbin.
Posted on 23 Aug. 2001 - New Annotation Tracks on April 2001 Browser
Tracks continue to be added to the
April 2001 browser.
Our old friend the Exofish track is back. The blat mouse homology
track is now up as well, computed at somewhat more sensitive settings
than it was in the December 2000 browser.
We've recently received some significant funding from NHGRI to
maintain and extend this site. This has allowed us among other things
to hire an artist, Jenny Draper, who is responsible for the new look.
Freeze-Specific News Archives
1 Apr. 2001 Freeze
13 Jul. 2001: fixed bug where some UTRs were
mis-annotated in the known genes on the minus strand.
12 Dec. 2000 Freeze
13 Jul. 2001: fixed bug where some UTRs were
mis-annotated in the known genes on the minus strand.
5 Apr. 2001: chromosome level files (but not contig level files)
updated to fix bug where some of the centromeres were misplaced
1 Apr. 2001: chromosome Y updated to fix a bug that put a large
gap between each clone. This bug was limited to the Y chromosome.
7 Oct. 2000 Freeze
7 Apr. 2001: Affymetrix gene predictions updated and available
for bulk download.
9 Jan. 2001: all files were updated after a bug that had caused
some finished clones to be flipped in the assembly was caught and fixed.
Our apologies for any inconvenience this has caused.
10 Nov. 2000: the sequence (.fa) files for two contigs:
X/ctg18523/ctg18523.fa and 7/ctg15082/ctg15082.fa were updated.
These files had null (zero valued) characters that have been
replaced with N characters. These characters were a result of
a mismatch between clone sizes in the map and in finished NT
contigs. The sequence for chromosomes X and 7, which contain
these contigs, has also been updated.
5 Sep. 2000 Freeze
11 Oct. 2000: chr21.agp and chr22.fa were updated. chr21.agp
was a version which went with the UCSC draft assembly rather than the
Sanger/NCBI final assembly of this chromosome. chr21.agp and chr21.fa
are now in sync. chr22.fa and chr22.agp were also previously out of
sync. chr22.fa was obtained from Sanger while chr22.agp had been obtained
by NCBI. With this update they are consistent, both NCBI versions.
Apologies for any rework this causes you.
9 Oct. 2000: chr21_random.* and chr22_random.* were removed from
the zip-files in the September 5th freeze. These files were relics that
should not have been included in the first place. The files
chr9_random.agp, chr10_random.agp, chr11_random.agp, chr12_random.agp,
chr13_random.agp and chr14_random.agp were updated. There was a bug
where the initial field of the initial lines in these files was
"(null)" rather than "chrN_random" as it should have been.
17 Jul. 2000 Freeze
22 Sep. 2000: The zip-files chromFa.zip and chromAgp.zip under the July 17th full data set
were updated to fix some duplications of clone contigs that occurred in the chrN_random.agp and chrN_random.fa
files contained within these zip-files. These "_random" files are files that contain clone contigs that were mapped to a particular chromosome, but
could not be placed at a specific position within that chromosome. They correspond to the "RANDOM" sections of the WashU map.
None of the regular chrN.agp or chrN.fa files were affected by this update, nor was any of the information in the
contigAgp.zip or contigFa.zip files changed. For convenience, we include two new files, chromRandAgp.zip and
chromRandFa.zip, for users who would like to download only the data that has changed. These zips consist of
the updated chrN_random.agp and chrN_random.fa files, respectively.
4 Sep. 2000: The files chromFa.zip and contigFa.zip under the
July 17th full data set and the files under July 17th data by individual clone contig
were updated to fix some incorrect (null(0))
characters that needed to be replaced by 'n' characters in some
Fasta files. The following contig Fasta files on chromosomes 1,8,11,12,16,
17 and 19 were affected:
