UCSC Genome Bioinformatics
  UCSC Genome Browser Acknowledgments

The data and software displayed on this site are the result of a large collaborative effort among many individuals at UCSC and at research institutions around the world. We'd like to acknowledge the scientists and engineers who have contributed to the UCSC Genome Browser and its data, and the organizations who have made this project possible through their generous funding.

Mammals

Other Vertebrates

Deuterostomes

Insects

Nematodes

Other

Viruses



  Human Genome Browser: Acknowledgments
HHMI CISI
NHGRI

The UCSC Human Genome Browser is generated by the UCSC Genome Bioinformatics Group in collaboration with the International Human Genome Project. The browser project is funded by grants from the National Human Genome Research Institute, and generous support from the Howard Hughes Medical Institute and the California Institutes for Science and Innovation.

We work with collaborators at many other institutions to produce and annotate this reference sequence of the human genome. To view complete acknowledgments for a specific annotation, see the "Credits" section on the track's description page in the Genome Browser. For a list of browser-related publications, see our publications page.

UCSC Human Genome Browsers:

  • hg38 (GRCh38): Hiram Clawson, Brian Raney, Robert Kuhn, Donna Karolchik, Steve Heitner
  • hg19 (GRCh37): Hiram Clawson, Brooke Rhead, Pauline Fujita, Ann Zweig, Katrina Learned, Donna Karolchik and Robert Kuhn
  • hg18: Engineering effort led by Fan Hsu; QA effort led by Ann Zweig
  • hg17: Hiram Clawson, Terry Furey, Heather Trumbower, Robert Kuhn, Donna Karolchik, Kate Rosenbloom, Angie Hinrichs, Rachel Harte, and Jim Kent
  • hg16: Terry Furey, Hiram Clawson, Heather Trumbower, Mark Diekhans, Robert Baertsch, Donna Karolchik, Jim Kent
  • hg15 (archived): 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 many other students in the UCSC Genome Bioinformatics group
  • Earlier browsers (archived): UCSC Genome Bioinformatics staff and students

  Human Genome: Data Sources

Starting with the hg19 (GRCh37) assembly, the human genome sequence is provided by the Genome Reference Consortium (GRC), 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.

Prior to hg19, the human genome sequence data used by the browser were generated by laboratories belonging to the Human Genome Sequencing Consortium. Periodic freezes of this data were generated by NCBI, and EST, mRNA, BACend and other types of data used for the assembly and annotation were obtained from GenBank, European Molecular Biology Lab (EMBL), and DNA Data Bank of Japan (DDBJ). Clone maps were created by the individual sequencing centers.

The original chromosome files were produced by the institutions and individuals listed in the table below.

Finished Chromosomes
Chr. # Sequencing Centers AGP File
1 The Sanger Institute, Cambridge, UK
University of Washington, Department of Genome Sciences, Seattle, WA, USA 		Jane Rogers
2 The Genome Institute at Washington University (WUSTL), St. Louis, MO, USA Rick Wilson
3 Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC), Houston, TX, USA
Beijing Genomics Institute/Human Genome Center, Beijing, China
University of Washington, Department of Genome Sciences, Seattle, WA, USA 		Steve Scherer
4 The Genome Institute at Washington University (WUSTL), St. Louis, MO, USA
Stanford Human Genome Center, Palo Alto, CA, USA 		Rick Wilson
5 Joint Genome Institute, U.S. Department of Energy, Walnut Creek, CA, USA
Stanford Human Genome Center, Palo Alto, CA, USA 		Jeremy Schmutz
6 The Wellcome Trust Sanger Institute, Cambridge, UK Jane Rogers
7 The Genome Institute at Washington University (WUSTL), St. Louis, MO USA
University of Washington, Department of Genome Sciences, Seattle, WA, USA 		Rick Wilson
8 The Broad Institute, Cambridge, MA USA
Keio University, Tokyo, Japan
Institute of Molecular Biology (IMB), Jena, Germany 		Chad Nusbaum
9 The Wellcome Trust Sanger Institute, Cambridge, UK
Gesellschaft fuer Biotechnologische Forschung (GBF), Braunschweig, Germany 		Jane Rogers
10 The Wellcome Trust Sanger Institute, Cambridge, UK
Genome Therapeutics Corporation (GTC), Waltham, MA, USA 		Jane Rogers
11 RIKEN Human Genome Research Group, Japan
The Broad Institute, Cambridge, MA USA 		Todd Taylor
12 Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC), Houston, TX, USA Steve Scherer
13 The Wellcome Trust Sanger Institute, Cambridge, UK Jane Rogers
14 Genoscope National Sequencing Centre, Evry, France
Institute for Systems Biology (ISB), Seattle, WA
The Genome Institute at Washington University (WUSTL), St. Louis, MO USA
RIKEN Human Genome Research Group, Japan 		Jean Weissenbach
15 The Broad Institute, Cambridge, MA USA
Institute of Molecular Biology (IMB),
Institute for Systems Biology (ISB), Seattle, WA 		Chad Nusbaum
16 Joint Genome Institute (JGI), U.S. Department of Energy, Walnut Creek, CA, USA
Stanford Human Genome Center, Palo Alto, CA, USA
The Institute for Genomic Research (TIGR), Rockville, MD, USA
The Wellcome Trust Sanger Institute, Cambridge, UK 		Jeremy Schmutz
17 The Broad Institute, Cambridge, MA USA Chad Nusbaum
18 The Broad Institute, Cambridge, MA USA
RIKEN Human Genome Research Group, Japan 		Chad Nusbaum
19 Joint Genome Institute (JGI), U.S. Department of Energy, Walnut Creek, CA, USA
Stanford Human Genome Center, Palo Alto, CA, USA 		Jeremy Schmutz
20 The Wellcome Trust Sanger Institute, Cambridge, UK James Gilbert
21 RIKEN Human Genome Research Group, Japan
Max Planck Institute for Molecular Genetics, Berlin, Germany
Gesellschaft fuer Biotechnologische Forschung (GBF), Braunschweig, Germany
Keio University School of Medicine, Tokyo, Japan
Chromosome 21 Consortium 		Todd Taylor
22 The Wellcome Trust Sanger Institute, Cambridge, UK
The University of Oklahoma, Norman, OK USA
Keio University School of Medicine, Tokyo, Japan 		Jane Rogers
X The Wellcome Trust Sanger Institute, Cambridge, UK
Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC), Houston, TX, USA
Institute of Molecular Biology (IMB), Jena, Germany
The Genome Institute at Washington University (WUSTL), St. Louis, MO USA
Max Planck Institute for Molecular Genetics, Berlin, Germany 		Jane Rogers
Y The Genome Institute at Washington University (WUSTL), St. Louis, MO USA Rick Wilson



  Alpaca Genome

The Alpaca Genome Browser is provided with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC Alpaca Genome Browser/Initial Annotations:
    • vicPac2: Hiram Clawson and Luvina Guruvadoo
    • vicPac1: Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik

The alpaca sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357

The alpaca data are provided with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Armadillo Genome

The Armadillo Genome Browser is provided with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC Armadillo Genome Browser/Initial Annotations:
    • dasNov3: Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik

The armadillo sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357

The armadillo data are provided with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Baboon Genome

The Baboon Genome Browser is provided by the Baboon Genome Sequencing Consortium with the following acknowledgments:

The baboon sequence is made freely available for public use by the Baboon Genome Sequencing Consortium. Please review the BCM-HGSC conditions for use guidelines before using this data.


  Bonobo Genome

The Bonobo Genome Browser is provided with the following acknowledgments:

The bonobo sequence is made freely available by the Max-Planck Institute for Evolutionary Anthropology.


  Brown kiwi Genome

The Brown kiwi Genome Browser is provided with the following acknowledgments:

The brown kiwi sequence is made freely available by the Max-Planck Institute for Evolutionary Anthropology.


  Bushbaby Genome

The Bushbaby Genome Browser is provided with the following acknowledgments:

The bushbaby sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357

The bushbaby data are provided with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Cat Genome

The UCSC felCat8 Genome Browser displays data from the Nov. 2014 Felis_catus_8.0 assembly of the domestic cat produced by the International Cat Genome Sequencing Consortium. This assembly was provided with the following acknowledgments:

The UCSC felCat5 Genome Browser displays data from the Sep. 2011 Felis_catus-6.2 assembly of the domestic cat produced by the International Cat Genome Sequencing Consortium. This assembly was provided with the following acknowledgments:

The UCSC felCat4 Genome Browser displays data from the Dec. 2008 catChrV17e draft assembly, based on sequence reads from six domestic cats and one wild cat. The browser is provided with the following acknowledgments:

The UCSC felCat3 Genome Browser displays data from the March 2006 v3 draft assembly of the domestic cat (Felis catus). This assembly was provided with the following acknowledgments:

The catChrV17e cat assembly was initially published in Pontius JU et al. Initial sequence and comparative analysis of the cat genome. Genome Res. 2007 Nov;17(11):1675-89. PMID 17975172; PMCID: PMC2045150

The Broad Institute released the initial 2X (v3) assembly of the cat genome as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357

The cat sequence is made freely available with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Chimpanzee Genome

The UCSC Chimpanzee Genome Browsers display draft assembly data produced by the Chimpanzee Genome Sequencing Consortium:

  • Feb. 2011 panTro4 browser: v2.1.4 chromosome-based 6X draft assembly
  • Oct. 2010 panTro3 browser: v2.1.3 chromosome-based 6X draft assembly
  • Mar. 2006 panTro2 browser: v2.1 chromosome-based 6X draft assembly (Oct. 2005)
  • Nov. 2003 panTro1 browser: v1.1 Arachne draft assembly

The Chimpanzee Genome Browsers have the following acknowledgments:

The initial sequencing and analysis of the chimpanzee genome was published by the Chimpanzee Sequencing and Analysis Consortium. The chimpanzee sequence data may be freely downloaded, used in analyses, and repackaged in databases if the provider is properly acknowledged. Please cite this publication when using these data:

The Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature. 2005 Sep 1;437(7055):69-87. PMID: 16136131


  Chinese Hamster Genome

The Chinese hamster assembly was provided by the Beijing Genomics Institution-Shenzhen with the following acknowledgments:

The Chinese hamster sequence data may be freely downloaded, used in analyses, and repackaged in databases if the provider is properly acknowledged. Please cite this publication when using these data:

Lewis NE, Liu X, Li Y, Nagarajan H, Yerganian G, O'Brien E, Bordbar A, Roth AM, Rosenbloom J, Bian C et al. Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome. Nat Biotechnol. 2013 Aug;31(8):759-65.


  Cow Genome

The UCSC Cow Genome Browser displays two different assemblies of the bovine genome: one provided by the University of Maryland Center for Bioinformatics and Computational Biology (UMD CBCB) and one from the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC). The assemblies available in the browser include:

  • Jun. 2014 (bosTau8) assembly - UMD CBCB version UMD_3.1.1
  • Oct. 2011 (bosTau7) assembly - Bovine Genome Sequencing Consortium (BCM-HGSC) version Btau_4.6.1
  • Nov. 2009 (bosTau6) assembly - UMD CBCB version UMD_3.1
  • Oct. 2007 (bosTau4) assembly - BCM-HGSC version Btau_4.0
  • Aug. 2006 (bosTau3) assembly - BCM-HGSC version Btau_3.1
  • Mar. 2005 (bosTau2) assembly - BCM-HGSC version Btau_2.0
  • Sep. 2004 (bosTau1) assembly - BCM-HGSC version Btau_1.0

The UMD CBCB genome assemblies are provided with the following acknowledgments:

The BCM-HGSC genome assemblies are provided with the following acknowledgments:

  • Funding - For a list of the many agencies that funded the cow sequencing project, see the BCM-HGSC Bovine Genome Project page.
  • BAC library DNA: Dr. Michael MacNeil's laboratory at the USDA Agricultural Research Service, Miles City, MT, USA
  • Whole genome shotgun sequence DNA: Dr. Timothy Smith's laboratory at the U.S. Meat Animal Research Center, Clay Center, NE, USA
  • BAC-based fingerprint map: Genome Sciences Centre, Vancouver, B.C.
  • UCSC Cow Genome Browser/Initial Annotations:
    • bosTau7: Chin Li, Hiram Clawson, Brian Raney and Steve Heitner
    • bosTau4: Hiram Clawson, Brian Raney, and Ann Zweig
    • bosTau3: Heather Trumbower, Angie Hinrichs, Kayla Smith and Donna Karolchik
    • bosTau2: Galt Barber, Brian Raney, Mark Diekhans, Jennifer Jackson, and Donna Karolchik
    • bosTau1 (archived): Heather Trumbower, Jim Kent, Hiram Clawson, Angie Hinrichs, Brian Raney, Mark Diekhans, Robert Kuhn, Ali Sultan-Qurraie and Donna Karolchik
The cow sequence data may be freely downloaded, used in analyses, and repackaged in databases if the provider is properly acknowledged. Please cite the appropriate publication when using these data.

UMD cow assembly:

Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F, Pertea G, Van Tassell CP, Sonstegard TS et al. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol. 2009;10(4):R42.

Baylor cow assembly:

Bovine Genome Sequencing and Analysis Consortium. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science. 2009 Apr 24;324(5926):522-8.

For more information see the UMD CBCB and the BCM-HGSC Bovine Genome Project pages.


  Crab-eating macaque Genome

The Crab-eating macaque Genome Browser is provided with the following acknowledgments:

The crab-eating macaque data are provided with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Dog Genome

The UCSC Dog Genome Browser displays assemblies of the domestic dog (Canis familiaris) with the following acknowledgments:

The dog genome sequence is made freely available by the Dog Genome Sequencing Project. Please cite this publication when using these data:

Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ 3rd, Zody MC et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature. 2005 Dec 8;438(7069):803-19. PMID: 16341006


  Dolphin Genome

The Dolphin Genome Browser is provided with the following acknowledgments:

The dolphin sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357

The dolphin data are provided with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Elephant Genome

The elephant assembly was provided by the Broad Institute with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC Elephant Genome Browser/Initial Annotations:
    • loxAfr3: Hiram Clawson, Pauline Fujita, Vanessa Swing, Antonio Coelho, and Donna Karolchik

The elephant sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.


  Ferret Genome

The ferret assembly was provided by the Ferret Genome Sequencing Consortium with the following acknowledgments:

  • Sequencing/Assembly: Ferret Genome Sequencing Consortium and The Broad Institute, Cambridge, MA, USA
  • UCSC Ferret Genome Browser/Initial Annotations:
    • musFur1: Hiram Clawson, Brian Lee, and Brooke Rhead

The ferret sequence data may be freely downloaded, used in analyses, and repackaged in databases if the provider is properly acknowledged. Please cite this publication when using these data:

Peng X, Alföldi J, Gori K, Eisfeld AJ, Tyler SR, Tisoncik-Go J, Brawand D, Law GL, Skunca N, Hatta M et al. The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease. Nat Biotechnol. 2014 Dec;32(12):1250-5.


  Gibbon Genome

The UCSC Gibbon Genome Browser displays data from the draft assemblies of the northern white-cheeked gibbon (Nomascus leucogenys) provided by the Gibbon Genome Sequencing Consortium with the following acknowledgments:

The gibbon sequence data may be freely downloaded, used in analyses, and repackaged in databases if the provider is properly acknowledged. Please cite this publication when using these data:

Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B et al. Gibbon genome and the fast karyotype evolution of small apes. Nature. 2014 Sep 11;513(7517):195-201.


  Gorilla Genome

The UCSC gorGor4 Genome Browser displays data from the Dec 2014 assembly of Gorilla gorilla gorilla produced by the Wellcome Trust Sanger Institute. This assembly is provided with the following acknowledgements:

  • Sequencing/Assembly: The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
  • UCSC Gorilla Genome Browser/Initial Annotations:
    • gorGor4: Hiram Clawson, Mark Diekhans, Brian Raney, Christopher Lee

The UCSC gorGor3 Genome Browser displays data from the May 2011 draft assembly of Gorilla gorilla gorilla. This assembly is provided with the following acknowledgments:

The gorilla sequence data may be freely downloaded, used in analyses, and repackaged in databases if the provider is properly acknowledged. Please cite this publication when using these data:

Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T et al. Insights into hominid evolution from the gorilla genome sequence. Nature. 2012 Mar 7;483(7388):169-75.


  Guinea Pig Genome

The guinea pig assembly (Cavia porcellus) is provided with the following acknowledgments:

The guinea pig sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.


  Hedgehog Genome

The Hedgehog Genome Browser is provided with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute at MIT and Harvard, Cambridge, MA, USA
  • UCSC Hedgehog Genome Browser/Initial Annotations:
    • eriEur2: Hiram Clawson, Brian Raney and Steve Heitner
    • eriEur1: Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik

The hedgehog sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357

The hedgehog data are provided with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Horse Genome

The UCSC Horse Genome Browser displays the draft assembly of the horse (Equus caballus) genome from The Broad Institute. This assembly is provided with the following acknowledgments:

The horse sequence data may be freely downloaded, used in analyses, and repackaged in databases if the provider is properly acknowledged. Please cite this publication when using these data:

Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear TL, Adelson DL, Bailey E, Bellone RR et al. Genome sequence, comparative analysis, and population genetics of the domestic horse. Science. 2009 Nov 6;326(5954):865-7.


  Kangaroo Rat Genome

The Kangaroo Rat Genome Browser is provided with the following acknowledgments:

The kangaroo rat sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357

The kangaroo rat data are provided with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Manatee Genome

The Manatee Genome Browser is provided with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC Manatee Genome Browser/Initial Annotations:
    • triMan1: Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik

The manatee genome sequence data are made available to the public with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.


  Marmoset Genome

The Marmoset Genome Browser is provided with the following acknowledgments:

These data were produced by The Genome Institute at WUSTL and the BCM-HGSC and can be downloaded here.

The marmoset sequence is made freely available before scientific publication with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. The centers producing the data reserve the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome.
  4. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects and the resulting NHGRI policy statement.
  5. Any redistribution of the data should carry this notice.


  Megabat Genome

The Megabat (Fruitbat) Genome Browser is provided with the following acknowledgments:

The megabat sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357

The megabat data are provided with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Microbat Genome

The microbat (little brown bat) genome is provided by The Broad Institute with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC Microbat Genome Browser/Initial Annotations:
    • myoLuc2: Chin Li, Brian Raney, Robert Kuhn, Steve Heitner, Brooke Rhead, Greg Roe and Donna Karolchik

The microbat genome sequence data are made available to the public with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.


  Minke whale Genome

The minke whale genome is provided by the Korea Institute of Ocean Science and Technology with the following acknowledgments:

The minke whale genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

Yim HS, Cho YS, Guang X, Kang SG, Jeong JY, Cha SS, Oh HM, Lee JH, Yang EC, Kwon KK et al. Minke whale genome and aquatic adaptation in cetaceans. Nat Genet. 2014 Jan;46(1):88-92. PMID: 24270359


  Mouse Genome

Starting with mm10 (GRCm38), the mouse genome assembly is now provided by the Genome Reference Consortium (GRC). See the GRC Mouse Genome web pages for acknowledgments.

Prior to mm10/GRCm38, mouse assemblies were produced by the Mouse Genome Sequencing Consortium, with these acknowledgments:

The initial 3X coverage of the mouse genome was produced by the Mouse Sequencing Consortium, with the following acknowledgments:

The mouse genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 Dec 5;420(6915):520-62. PMID: 12466850

For more information about mouse assemblies provided by the GRC, see the GRC mouse genome web pages. For information about assemblies prior to mm10/GRCm38, see the Wellcome Trust Sanger Institute Mouse Resources Portal.

  Mouse Lemur Genome

The Mouse Lemur Genome Browser is provided with the following acknowledgments:

The mouse lemur sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357

The mouse lemur data are provided with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Naked Mole-rat Genome

The naked mole-rat genome was provided with the following acknowledgments:

  • Sequencing/Assembly: Beijing Genomics Institute, Shenzhen, China
  • UCSC Naked Mole-rat Genome Browser/Initial Annotations:
    • hetGla2: Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
    • hetGla1: Chin Li and Luvina Guruvadoo

The naked mole-rat genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

Keane M, Craig T, Alföldi J, Berlin AM, Johnson J, Seluanov A, Gorbunova V, Di Palma F, Lindblad-Toh K, Church GM et al. The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations. Bioinformatics. 2014 Dec 15;30(24):3558-60.


  Opossum Genome

The opossum genome assembly (Monodelphis domestica) is provided by The Broad Institute with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • FISH Mapping: North Carolina State University (NCSU), Raleigh, NC, USA
  • UCSC Opossum Genome Browser/Initial Annotations:
    • monDom5: Andy Pohl, Hiram Clawson, Brian Raney, Mark Diekhans, Brooke Rhead and Katrina Learned
    • monDom4: Hiram Clawson, Archana Thakkapallayil, Ann Zweig, Kayla Smith and Donna Karolchik
    • monDom1: Hiram Clawson, Galt Barber, Ali Sultan-Qurraie, Brian Raney and Donna Karolchik

The opossum genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A et al. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature. 2007 May 10;447(7141):167-77.


  Orangutan Genome

The Sumatran orangutan genome assembly (Pongo pygmaeus abelii) is provided with the following acknowledgments:

  • Sequencing:
  • Sequence Assembly and Chromosomal Sequence/AGP Construction: The Genome Institute at WUSTL
  • DNA Source: Dr. Greely Stones, Gladys Porter Zoo, Brownsville, TX, USA
  • BAC Library: Yuko Yoshonaga in Pieter de Jong's laboratory, Children's Hospital Oakland Research Institute, Oakland, CA, USA
  • Fosmid Library: The Genome Institute at WUSTL
  • Fingerprint Map: The Genome Institute at WUSTL
  • Cytogenetic Mapping and Human/Orangutan Breakpoint Analyses: Mariano Rocchi, Department of Genetics and Microbiology, University of Bari, Bari, Italy
  • Fosmid End Placement against the Human Genome (used for breakpoint/inversion analyses during AGP construction): Lin Chen and Evan Eichler, Department of Genome Sciences, University of Washington, Seattle, WA, USA
  • Funding: National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH)
  • UCSC Orangutan Genome Browser/Initial Annotations:
    • ponAbe2: Hiram Clawson, Kayla Smith, Robert Kuhn, Ann Zweig and Donna Karolchik

The orangutan genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P et al. Comparative and demographic analysis of orang-utan genomes. Nature. 2011 Jan 27;469(7331):529-33.


  Panda Genome

The panda (Ailuropoda melanoleuca) assembly was provided by BGI-Shenzhen with the following acknowledgments:

The panda genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z et al. The sequence and de novo assembly of the giant panda genome. Nature. 2010 Jan 21;463(7279):311-7. PMID: 20010809


  Pig Genome

The pig (Sus scrofa) assembly was provided with the following acknowledgments:

The International Swine Genome Sequencing Consortium genome-wide analyses of the pig genome is described in:

Uenishi H, Morozumi T, Toki D, Eguchi-Ogawa T, Rund LA, Schook LB. Large-scale sequencing based on full-length-enriched cDNA libraries in pigs: contribution to annotation of the pig genome draft sequence. BMC Genomics. 2012 Nov 15;13:581. PMID: 23150988

The pig genome data is made freely available with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. The centers producing the data reserve the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.


  Pika Genome

The pika genome assembly (Ochotona princeps) is provided with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC Pika Genome Browser/Initial Annotations:
    • ochPri3: Hiram Clawson, Brian Raney, and Steve Heitner
    • ochPri2: Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik

The pika sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357

The pika data are provided with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Platypus Genome

The platypus genome assembly (Ornithorhynchus anatinus) is provided with the following acknowledgments:

The platypus genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT et al. Genome analysis of the platypus reveals unique signatures of evolution. Nature. 2008 May 8;453(7192):175-83. PMID: 18464734


  Rabbit Genome

The rabbit genome assembly (Oryctolagus cuniculus) is provided with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC Rabbit Genome Browser/Initial Annotations:
    • oryCun2: Hiram Clawson and Antonio Coelho

The rabbit genome data are made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. The centers producing the data reserve the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.


  Rat Genome

The rat genome assembly (Rattus norvegicus) is provided by the Rat Genome Sequencing Consortium with the following acknowledgments:

The rat genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite these publications when using these data:

Havlak P, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Weinstock GM, Gibbs RA. The Atlas genome assembly system. Genome Res. 2004 Apr;14(4):721-32. PMID: 15060016

Rat Genome Sequencing Project Consortium. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 Apr 1;428(6982):493-521. PMID: 15057822

See the Baylor conditions of use web page for restrictions on the use of these data.


  Rhesus Macaque Genome

The UCSC Genome Browser displays multiple assemblies of the Rhesus macaque genome produced by different institutions:

The BGI assembly is provided with the following acknowledgments:

  • Funding: Southern China Center for Innovative Pharmaceuticals (SCCIP), the National Natural Science Foundation of China, the Shenzhen Municipal Government of China, the Major State Basic Research Development Program of China, the National Basic Research Program of China, and the National Science and Technology Major Project of Key Drug Innovation and Development
  • Sequencing/Assembly: BGI, Shenzhen, China

The MMGSC assembly is provided with the following acknowledgments:

For more information on the MMGSC rhesus macaque genome project, see the BCM HGSC Rhesus Monkey Genome Project web page.

  • UCSC Rhesus Genome Browser/Initial Annotations:
    • rheMac8: Hiram Clawson, Christopher Lee, and Cath Tyner
    • rheMac3: Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
    • rheMac2: Robert Baertsch, Kayla Smith, Ann Zweig, Robert Kuhn, and Donna Karolchik
    • rheMac1 (archived): Robert Baertsch, Galt Barber, and Donna Karolchik

The initial sequencing and analysis of the rhesus macaque genome produced by the MMGSC was published in: Rhesus Macaque Genome Sequencing and Analysis Consortium. Evolutionary and Biomedical Insights from the Rhesus Macaque Genome. Science. 2007 Apr 13;316(5822):222-34. PMID: 17431167

The initial sequencing and analysis of the rhesus macaque genome produced by BGI was published in: Yan G, Zhang G, Fang X, Zhang Y, Li C, Ling F, Cooper DN, Li Q, Li Y, van Gool AJ et al Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nat Biotechnol. 2011 Oct 16;29(11):1019-23. PMID: 22002653

The rhesus macaque sequence is made freely available for public use with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged. For the rheMac1 and rheMac2 data, please cite the BCM-HGSC web site or publications from BCM-HGSC referring to the genome sequence.
  3. The BCM-HGSC and RMGSC plan to publish the assembly and genomic annotation of the dataset, including large-scale identification of regions of evolutionary conservation.
  4. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects and the resulting NHGRI policy statement.
  5. Any redistribution of the data should carry this notice.


  Rock Hyrax Genome

The rock hyrax genome assembly (Procavia capensis) is provided with the following acknowledgments:

The rock hyrax sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357

The rock hyrax data are provided with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Sheep Genome

The sheep genome assembly (Ovis aries) is provided by the International Sheep Genomics Consortium (ISGC) with the following acknowledgments:

The sheep genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite these publications when using these data:

Jiang Y, Xie M, Chen W, Talbot R, Maddox JF, Faraut T, Wu C, Muzny DM, Li Y, Zhang W et al. The sheep genome illuminates biology of the rumen and lipid metabolism. Science. 2014 Jun 6;344(6188):1168-73. PMID: 24904168

International Sheep Genomics Consortium. The sheep genome reference sequence: a work in progress. Anim Genet. 2010 Oct;41(5):449-53. PMID: 20809919


  Shrew Genome

The common shrew genome assembly (Sorex araneus) is provided with the following acknowledgments:

The shrew sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357

The shrew data are provided with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Sloth Genome

The sloth genome assembly (Choloepus hoffmanni) is provided with the following acknowledgments:

The sloth sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357

The sloth data are provided with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Squirrel Genome

The squirrel genome assembly (Spermophilus tridecemlineatus)) is provided with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC Squirrel Genome Browser/Initial Annotations:
    • speTri2: Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik

The squirrel sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357

The squirrel data are provided with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Squirrel Monkey Genome

The squirrel monkey genome assembly (Saimiri boliviensis) is provided with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC Squirrel Monkey Genome Browser/Initial Annotations:
    • saiBol1: Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik

The squirrel monkey genome sequence data are made available to the public with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.


  Tarsier Genome

The tarsier genome assembly (Tarsius syrichta) is provided with the following acknowledgments:

The tarsier sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357

The tarsier data are provided with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Tasmanian Devil Genome

The Tasmanian devil genome assembly (Sarcophilus harrisii) is provided with the following acknowledgments:

The Tasmanian devil genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

Murchison EP, Schulz-Trieglaff OB, Ning Z, Alexandrov LB, Bauer MJ, Fu B, Hims M, Ding Z, Ivakhno S, Stewart C et al. Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer. Cell. 2012 Feb 17;148(4):780-91. PMID: 22341448


  Tenrec Genome

The tenrec genome assembly (Echinops telfairi) is provided by The Broad Institute with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC Tenrec Genome Browser/Initial Annotations:
    • echTel2: Hiram Clawson, Brian Raney and Steve Heitner
    • echTel1: Hiram Clawson, Brian Raney and Steve Heitner

The tenrec genome sequence data are made available to the public with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.


  Tree Shrew Genome

The tree shrew genome assembly (Tupaia belangeri) is provided with the following acknowledgments:

The tree shrew sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357

The tree shrew data are provided with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Wallaby Genome

The wallaby genome assembly (Macropus eugenii) is provided with the following acknowledgments:

The wallaby genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G et al. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol. 2011 Aug 29;12(8):R81. PMID: 21854559


  White Rhinoceros Genome

The southern white rhinoceros genome assembly (Ceratotherium simum) is provided with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • Data Samples: Dr. Oliver Ryder, San Diego Zoo Institute for Conservation Research, San Diego, CA
  • UCSC White Rhinoceros Genome Browser/Initial Annotations:
    • cerSim1: Hiram Clawson and Steve Heitner

The southern white rhinoceros sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. The centers producing the data reserve the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.


  American Alligator Genome

The American alligator assembly (Alligator mississippiensis) is provided by the International Crocodilian Genomes Working Group with the following acknowledgments:

The American alligator genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

St John JA, Braun EL, Isberg SR, Miles LG, Chong AY, Gongora J, Dalzell P, Moran C, Bed'hom B, Abzhanov A et al. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biol. 2012 Jan 31;13(1):415. PMID: 22293439


  Atlantic Cod Genome

The Atlantic cod genome assembly (Gadus morhua) is provided with the following acknowledgments:

  • Funding: Research Council of Norway (FUGE)
  • Sequencing/Assembly: GenoFisk Consortium
  • UCSC Atlantic Cod Genome Browser/Initial Annotations:
    • gadMor1: Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik

The Atlantic cod genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite these publications when using these data:

Johansen SD, Coucheron DH, Andreassen M, Karlsen BO, Furmanek T, Jørgensen TE, Emblem A, Breines R, Nordeide JT, Moum T et al. Large-scale sequence analyses of Atlantic cod. N Biotechnol. 2009 Jun;25(5):263-71. PMID: 19491044

Star B, Nederbragt AJ, Jentoft S, Grimholt U, Malmstrøm M, Gregers TF, Rounge TB, Paulsen J, Solbakken MH, Sharma A et al. The genome sequence of Atlantic cod reveals a unique immune system. Nature. 2011 Aug 10;477(7363):207-10. PMID: 21832995


  Budgerigar Genome

The budgerigar genome assembly (Melopsittacus undulatus) is provided with the following acknowledgments:

  • Sequencing/Assembly: The Genome Institute at Washington University (WUSTL), St. Louis, MO, USA
  • UCSC Budgerigar Genome Browser/Initial Annotations:
    • melUnd1: Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik

The budgerigar sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. The centers producing the data reserve the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome.
  4. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects and the resulting NHGRI policy statement.
  5. Any redistribution of the data should carry this notice.


  Chicken Genome

The chicken genome assembly (Gallus gallus) is provided with the following acknowledgments:

  • Sequencing: The Genome Institute at Washington University (WUSTL), St. Louis, MO, USA
  • Physical Map: The Genome Institute at WUSTL
  • Genetic Mapping/Linkage Analysis: The Chicken Mapping Consortium:
    • Wageningen Map based on Wageningen broilerxbroiler mapping population ("W" linkage maps; 460 F2 animals), coordinated by Martien Groenen, Wageningen University, Wageningen, The Netherlands
    • East Lansing Map based on the RJFxlayer cross ("E" linkage maps; 56 BC animals), coordinated by Hans Cheng, USDA-ARS, East Lansing, MI, USA
    • Compton map based on layerxlayer cross ("C" linkage maps; 52 BC animals), coordinated by Nat Bumstead, Institute for Animal Health
    • Consensus linkage map: Martien Groenen and Richard Crooijmans, Wageningen University
    • RH map: coordinated by Mireille Morisson and Alain Vignal, French National Institute for Agricultural Research (INRA), Toulouse
    • Linkage Mapping: White Leghorn X Red Junglefowl (800 F2 animals), coordinated by Susanne Kerje, Lina Jacobsson and Leif Andersson, Uppsala University, Uppsala, Sweden
    • Clone/Marker Pairs: coordinated by Jerry Dodgson, Michigan State University, East Lansing, MI, USA
    • Marker Name/Sequence Resolution: coordinated by Hans Cheng, USDA-ARS, East Lansing, MI, USA
    • Chicken FPC browser: ChickFPC, Martien Groenen and Richard Crooijmans (galGal3), Jan Aerts (galGal2), Wageningen University
    • Additional Mapping Data Contributions: Winston Bellott, David Page Lab, Whitehead Institute for Biomedical Research (WIBR-MIT), Cambridge, MA, USA
  • cDNA sequences: National Institutes of Health and The University of Manchester BBSRC ChickEST Database
  • RJF finished clones:
  • Assembly, Assembly/Map Integration, Golden Path Creation: The Genome Institute at WUSTL
  • SNPs and cross-referenced gene annotations: The Beijing Genomics Institute (BGI), Beijing, China
  • UCSC Chicken Genome Browser/Initial Annotations:
    • galGal4: Hiram Clawson, Brian Raney and Steve Heitner
    • galGal3: Angie Hinrichs, Kayla Smith, Donna Karolchik
    • galGal2: Angie Hinrichs, Heather Trumbower, Rachel Harte, Donna Karolchik

The chicken genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

International Chicken Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004 Dec 9;432(7018):695-716. PMID: 15592404

The BGI gene annotations and SNP data are made available with the following terms of use:

  1. Users are free to use these data in scientific papers analyzing particular genes, if the Beijing Genomics Institute (BGI) is acknowledged.
  2. BGI and its collaborators reserve the right to publish the initial analyses of these data, including but not restricted to the large-scale identification of functional polymorphisms, evolutionary patterns and signs of selection, correlations with known QTLs, utility of data for genetic mapping purposes, etc.
  3. Any redistribution of these data should carry this notice.

  Coelacanth Genome

The coelacanth genome assembly (Latimeria chalumnae) is provided with the following acknowledgments:

The coelacanth genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

Amemiya CT, Alföldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N et al. The African coelacanth genome provides insights into tetrapod evolution. Nature. 2013 Apr 18;496(7445):311-6. PMID: 23598338


  Elephant Shark Genome

The elephant shark genome assembly (Callorhinchus milii) is provided by the Singapore Institute of Molecular and Cell Biology with the following acknowledgments:

The elephant shark genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

Venkatesh B, Lee AP, Ravi V, Maurya AK, Lian MM, Swann JB, Ohta Y, Flajnik MF, Sutoh Y, Kasahara M et al. Elephant shark genome provides unique insights into gnathostome evolution. Nature. 2014 Jan 9;505(7482):174-9. PMID: 24402279


  Fugu Genome

The Fugu genome assembly (Takifugu rubripes) is provided by the U.S. 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). The assembly has the following acknowledgments:

  • Sequencing/Assembly: Assembly was constructed with the JGI assembler, JAZZ, from paired end sequencing reads produced by JGI and the IMCB at JGI, Myriad Genetics, and Celera Genomics
  • UCSC Fugu Genome Browser/Initial Annotations:
    • fr3: Hiram Clawson and Greg Roe
    • fr2: Cory McClean, Hiram Clawson, Ann Zweig, and Donna Karolchik
    • fr1: Kate Rosenbloom, Heather Trumbower, Robert Kuhn, and Donna Karolchik

The Fugu genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

Kai W, Kikuchi K, Tohari S, Chew AK, Tay A, Fujiwara A, Hosoya S, Suetake H, Naruse K, Brenner S et al. Integration of the genetic map and genome assembly of fugu facilitates insights into distinct features of genome evolution in teleosts and mammals. Genome Biol Evol. 2011;3:424-42. PMID: 21551351


  Lamprey Genome
The lamprey genome assembly (Petromyzon marinus) is provided with the following acknowledgments:

The lamprey genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD, Manousaki T, Meyer A et al. Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat Genet. 2013 Apr;45(4):415-21, 421e1-2. PMID: 234350859


  Lizard Genome

The lizard genome assembly (Anolis carolinensis) is provided by The Broad Institute with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA USA
  • UCSC Lizard Genome Browser/Initial Annotations:
    • anoCar2: Hiram Clawson, Brian Raney, Luvina Guruvadoo, and Donna Karolchik
    • anoCar1: Hiram Clawson, Archana Thakkapallayil, Robert Kuhn, and Donna Karolchik

The lizard genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

Alföldi J, Di Palma F, Grabherr M, Williams C, Kong L, Mauceli E, Russell P, Lowe CB, Glor RE, Jaffe JD et al. The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature. 2011 Aug 31;477(7366):587-91. PMID: 21881562


  Medaka Genome

The medaka genome assembly (Oryzias latipes) is provided by Japan's National Institute of Genetics (NIG) and the University of Tokyo. The assembly was constructed using the RAMEN assembler.

NOTE: The UCSC oryLat1 assembly was replaced by oryLat2 in Nov. 2008 to correct a UCSC assembly error with chrUn in which the gap relationships between contigs within their ultracontigs were broken. The oryLat2 assembly is based on the same assembly as oryLat1: the v1.0 assembly from NIG and the University of Tokyo.

  • Sequencing/Assembly: NIG and University of Tokyo, Japan
  • UCSC Medaka Genome Browser/Initial Annotations:
    • oryLat2: Hiram Clawson, Pauline Fujita, and Donna Karolchik

The medaka genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

Kasahara M, Naruse K, Sasaki S, Nakatani Y, Qu W, Ahsan B, Yamada T, Nagayasu Y, Doi K, Kasai Y et al. The medaka draft genome and insights into vertebrate genome evolution. Nature. 2007 Jun 7;447(7145):714-9. PMID: 17554307


  Medium Ground Finch Genome

The medium ground finch genome assembly (Geospiza fortis) is the product of a collaboration between the Genome 10K Project and Beijing Genomics Institute (BGI). The data are provided with the following acknowledgments:

  • Sequencing/Assembly: Genome 10K Project and Beijing Genomics Institute (BGI)
  • UCSC Medium Ground Finch Genome Browser/Initial Annotations:
    • geoFor1: Hiram Clawson and Greg Roe

The medium ground finch sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.

  Nile Tilapia Genome

The Nile tilapia genome assembly (Oreochromis niloticus) is provided with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC Nile Tilapia Genome Browser/Initial Annotations:
    • oreNil2: Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik

The Nile Tilapia genome sequence data are made available to the public with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.


  Painted Turtle Genome

The painted turtle genome assembly (Chrysemys picta bellii) is provided with the following acknowledgments:

  • Sequencing/Assembly: International Painted Turtle Genome Sequencing Consortium
  • UCSC Painted Turtle Genome Browser/Initial Annotations:
    • chrPic1: Hiram Clawson, Brian Raney and Steve Heitner

The painted turtle genome sequence data are made available to the public with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.


  Stickleback Genome

The stickleback genome assembly (Gasterosteus aculeatus) is provided by The Broad Institute with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA USA
  • UCSC Stickleback Genome Browser/Initial Annotations:
    • gasAcu1: Angie Hinrichs, Hiram Clawson, Kayla Smith, and Donna Karolchik

The stickleback sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.


  Tetraodon Genome

The Tetraodon genome assembly (Tetraodon nigroviridis) is provided with the following acknowledgments:

The Tetraodon genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

Yue GH, Lo LC, Zhu ZY, Lin G, Feng F. The complete nucleotide sequence of the mitochondrial genome of Tetraodon nigroviridis. DNA Seq. 2006 Apr;17(2):115-21.


  Turkey Genome

The turkey genome assembly (Meleagris gallopavo) is provided with the following acknowledgments:

The turkey genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg Le Ann, Bouffard P, Burt DW, Crasta O, Crooijmans RP et al. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol. 2010 Sep 7;8(9). PMID: 20838655


  X. tropicalis Genome

The Xenopus (Silurana) tropicalis genome assembly is provided by the U.S. DOE Joint Genome Institute (JGI) with the following acknowledgments:

  • Sequencing/Assembly: JGI, Walnut Creek, CA, USA
  • UCSC X. tropicalis Genome Browser/Initial Annotations:
    • xenTro7: Hiram Clawson, Brian Raney, and Matthew Speir
    • xenTro3: Hiram Clawson, Brian Raney, Brooke Rhead, Greg Roe, Steve Heitner, and Donna Karolchik
    • xenTro2: Angie Hinrichs, Kayla Smith, Robert Kuhn, and Donna Karolchik
    • xenTro1: Fan Hsu, Jim Kent, Heather Trumbower, Hiram Clawson, Brian Raney, Galt Barber, Mark Diekhans, Angie Hinrichs, and Donna Karolchik

The X. tropicalis genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L et al. The genome of the Western clawed frog Xenopus tropicalis. Science. 2010 Apr 30;328(5978):633-6. PMID: 20431018


  Zebra Finch Genome

The zebra finch genome assembly (Taeniopygia guttata) is provided by the Genome Institute at Washington University (WUSTL) with the following acknowledgments:

  • Sequencing/Assembly: The Genome Institute at WUSTL, St. Louis, MO, USA
  • Zebra finch DNA: Arthur P. Arnold lab, Dept. of Physiological Science, UCLA, Los Angeles, CA, USA
  • UCSC Zebra Finch Genome Browser/Initial Annotation:
    • taeGut2: Hiram Clawson, Brian Raney, and Steve Heitner
    • taeGut1: Brian Raney, Kayla Smith, Pauline Fujita, and Donna Karolchik

The zebra finch genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S et al. The genome of a songbird. Nature. 2010 Apr 1;464(7289):757-62. PMID: 20360741


  Zebrafish Genome

Starting with the danRer10 (GRCz10) assembly, the zebrafish genome sequence is now provided by the Genome Reference Consortium (GRC).

Prior assemblies have the following acknowledgments:

  • Sequencing/Assembly: The Wellcome Trust Sanger Institute, UK.
  • FPC map:
  • BAC Clones, BAC End Pairs:
    • The Wellcome Trust Sanger Institute, UK - GenBank accessions for BAC clones
    • Max-Planck Institute for Developmental Biology, Germany - BAC end pairs sequence data
    • Hubrecht Laboratory, Netherlands Institute for Developmental Biology, The Netherlands - BAC end pairs sequence data
  • Annotations:
  • UCSC Zebrafish Genome Browsers:
    • danRer10: Hiram Clawson, Brian Raney, Steve Heitner
    • danRer7: Hiram Clawson, Mary Goldman, Greg Roe, Brian Raney, Donna Karolchik
    • danRer6: Galt Barber, Robert Kuhn, Katrina Learned, Donna Karolchik
    • danRer5: Rachel Harte, Ann Zweig, Donna Karolchik
    • danRer4: Rachel Harte, Archana Thakkapallayil, Robert Kuhn, Ann Zweig, Donna Karolchik
    • danRer3: Rachel Harte, Jennifer Jackson, Ann Zweig, Ali Sultan-Qurraie, Donna Karolchik
    • danRer2 (archived): Rachel Harte, Mark Diekhans, Heather Trumbower, Donna Karolchik, Jennifer Jackson

The zebrafish genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, Collins JE, Humphray S, McLaren K, Matthews L et al. The zebrafish reference genome sequence and its relationship to the human genome. Nature. 2013 Apr 25;496(7446):498-503. PMID: 23594743

For more information about zebrafish assemblies provided by the GRC, see the GRC zebrafish web pages. For information about assemblies prior to danRer10/GRCz10, see the Sanger Institute's Danio rerio Sequencing Project web page.


  C. intestinalis Genome

The C. intestinalis v1.0 and v2.0 draft assemblies are provided by the U.S. DOE Joint Genome Institute (JGI) with the following acknowledgments:

The C. intestinalis sequence data have been freely provided by the JGI and may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM et al. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science. 2002 Dec 13;298(5601):2157-67. PMID: 12481130

For more information about the C. intestinalis assembly, see the JGI C. intestinalis portal.


  Lancelet Genome

The lancelet (Branchiostoma floridae) genome assembly is provided by the DOE Joint Genome Institute (JGI) with the following acknowledgments:

  • Funding: U.S. Department of Energy Office of Science, Biological and Environmental Research Program
  • Sequencing/Assembly: JGI
  • UCSC Lancelet Genome Browser/Initial Annotations:
    • braFlo1: Hiram Clawson, Ann Zweig, Pauline Fujita, Donna Karolchik

The lancelet genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK et al. The amphioxus genome and the evolution of the chordate karyotype. Nature. 2008 Jun 19;453(7198):1064-71. doi: 10.1038/nature06967. PMID: 18563158


  S. purpuratus Genome

The sea urchin (Strongylocentrotus purpuratus) genome assembly is provided by the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC). The assemblies available in the browser include:

  • Sep. 2006 strPur2 browser: Baylor version Spur 2.1 (NCBI v2.1)
  • Apr. 2005 strPur1 browser: Baylor version Spur_0.5 (NCBI v1.1)

These data are provided with the following acknowledgments:

The sea urchin genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:

Sea Urchin Genome Sequencing Consortium. The genome of the sea urchin Strongylocentrotus purpuratus. Science. 2006 Nov 10;314(5801):941-52. PMID: 17095691

For more information on the sea urchin genome project, see the BCM-HGSC Sea Urchin Genome Project web page.


  A. gambiae Genome

The MOZ2 Anopheles gambiae data were provided by the International Anopheles Genome Project and downloaded from Ensembl. The data have the following acknowledgments:

The A. gambaie sequence is made freely available by the International Anopheles Genome Project. Please cite the following publication when using these data:

Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R et al. The genome sequence of the malaria mosquito Anopheles gambiae. Science. 2002 Oct 4;298(5591):129-49. PMID: 12364791


  A. mellifera Genome

The Amel_1.2 data were provided by the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC) with the following acknowledgments:

The A. mellifera sequence is made freely available by the Honeybee Genome Sequencing Consortium. Please cite the following publication when using these data:

Honeybee Genome Sequencing Consortium. Insights into social insects from the genome of the honeybee Apis mellifera. Nature. 2006 Oct 26;443(7114):931-49. PMID: 17073008

See the Baylor conditions of use statement for guidelines regarding the use of these data.


  D. ananassae Genome

The droAna2 data were provided by Agencourt Bioscience. The droAna1 data were produced by the Institute for Genomic Research (TIGR). The D. ananassae Genome Browser has the following acknowledgments:

  • Sequencing: Agencourt Bioscience, Danvers, MA, USA
  • Assembly:
  • UCSC D. ananassae Genome Browser (droAna2): Angie Hinrichs, Brian Raney, Ann Zweig, Kayla Smith, and Donna Karolchik
  • UCSC D. ananassae Genome Browser (droAna1): Angie Hinrichs, Brian Raney, Heather Trumbower, Ali Sultan-Qurraie, and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

These data have been freely provided by Agencourt Bioscience before publication for use in the UCSC Genome Browser with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Agencourt Bioscience reserves the right to publish the initial large-scale analyses of the dataset, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly.
  4. Any redistribution of the data should carry this notice.

  D. erecta Genome
The droEre1 data were provided by Agencourt Bioscience. The D. erecta Genome Browser has the following acknowledgments:

These data have been freely provided by Agencourt Bioscience before publication for use in the UCSC Genome Browser with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Agencourt Bioscience reserves the right to publish the initial large-scale analyses of the dataset, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly.
  4. Any redistribution of the data should carry this notice.

  D. grimshawi Genome
The droGri data were provided by Agencourt Bioscience. The D. grimshawi Genome Browser has the following acknowledgments:
  • Sequencing and Assembly: Agencourt Bioscience, Danvers, MA, USA, using the Arachne assembler
  • UCSC D. grimshawi Genome Browser (droGri1): Angie Hinrichs, Brian Raney, Jennifer Jackson, Kayla Smith and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

These data have been freely provided by Agencourt Bioscience before publication for use in the UCSC Genome Browser with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Agencourt Bioscience reserves the right to publish the initial large-scale analyses of the dataset, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly.
  4. Any redistribution of the data should carry this notice.

  D. melanogaster Genome

The D. melanogaster assemblies displayed in the UCSC Genome Browser were obtained from the Berkeley Drosophila Genome Project (BDGP) with the following acknowledgments:

  • Sequencing and Assembly:
  • Annotations:
    • Euchromatic regions - FlyBase
    • Heterochromatic regions - DHGP, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
  • UCSC D. melanogaster Genome Browser and additional annotations (dm6): Hiram Clawson, Angie Hinrichs, and Matthew Speir
  • UCSC D. melanogaster Genome Browser and additional annotations (dm3): Angie Hinrichs, Archana Thakkapallayil, Kayla Smith, and Donna Karolchik - UCSC Genome Bioinformatics Group, UCSC, Santa Cruz, CA, USA
  • UCSC D. melanogaster Genome Browser and additional annotations (dm2): Angie Hinrichs, Brian Raney, Galt Barber, and Donna Karolchik - UCSC Genome Bioinformatics Group, UCSC, Santa Cruz, CA, USA
  • UCSC D. melanogaster Genome Browser and additional annotations (dm1): Angie Hinrichs, Brian Raney, Heather Trumbower, Ali Sultan-Qurraie, and Donna Karolchik - UCSC Genome Bioinformatics Group, UCSC, Santa Cruz, CA, USA

For additional information about these data, including citation guidelines, see the BDGP web site.

  D. mojavensis Genome

These data were produced by Agencourt Bioscience. The D. mojavensis Genome Browser has the following acknowledgments:

These data have been freely provided by Agencourt Bioscience before publication for use in the UCSC Genome Browser with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Agencourt Bioscience reserves the right to publish the initial large-scale analyses of the dataset, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly.
  4. Any redistribution of the data should carry this notice.

  D. persimilis Genome

The droPer1 assembly was provided with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC D. persimilis Genome Browser (droPer1): Angie Hinrichs, Kayla Smith, Robert Kuhn, Jennifer Jackson and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

The D. persimilis sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.


  D. pseudoobscura Genome

These data were produced by the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC). The D. pseudoobscura Genome Browser has the following acknowledgments:

  • Sequencing and Assembly: BCM-HGSC, Houston, TX, USA
  • UCSC D. pseudoobscura Genome Browser (dp3): Angie Hinrichs, Brian Raney, Jennifer Jackson and Donna Karolchik
  • UCSC D. pseudoobscura Genome Browser (dp2): Angie Hinrichs, Heather Trumbower, Robert Kuhn, Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

The D. pseudoobscura data are made available with specific conditions for use.


  D. sechellia Genome

The droSec1 assembly was provided with the following acknowledgments:

The D. sechellia sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.


  D. simulans Genome

These data were provided with the following acknowledgments:

The D. simulans sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. The centers producing the data reserve the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome.
  4. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects and the resulting NHGRI policy statement.
  5. Any redistribution of the data should carry this notice.


  D. virilis Genome

These data were produced by Agencourt Bioscience. The D. virilis Genome Browser has the following acknowledgments:

These data have been freely provided by Agencourt Bioscience before publication for use in the UCSC Genome Browser with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Agencourt Bioscience reserves the right to publish the initial large-scale analyses of the dataset, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly.
  4. Any redistribution of the data should carry this notice.

  D. yakuba Genome

These data were provided by The Genome Institute at Washington University (WUSTL) with the following acknowledgments:

The D. yakuba sequence is made freely available before scientific publication by The Genome Institute at WUSTL with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. The Drosophila yakuba analysis group is aiming to publish an initial analysis of the D. yakuba genome sequence in 2005 (submitted in early 2005) that will include descriptions of the assembly, genome landscape, comparative analysis and initial gene content. People who would like to coordinate other genome-wide analysis with this work should contact Richard K. Wilson, Genome Sequencing Center Director, Washington University School of Medicine. We welcome a coordinated approach to describing this community resource.
  4. Any redistribution of the data should carry this notice.

  C. elegans Genome

The C. elegans data was obtained from WormBase. We'd like to thank The Genome Institute at Washington University (WUSTL) and the Sanger Institute for their collaborative work on sequencing the C. elegans genome, and the WormBase consortium for providing access to the current C. elegans sequence.


  Worm Genomes (other than C. elegans)

The latest versions of the C. brenneri, C. briggsae, C. japonica, C. remanei, and P. pacificus sequences were obtained from the Genome Sequencing Center at The Genome Institute at Washington University (WUSTL). The cb1 browser data were obtained from WormBase.

We'd like to thank WUSTL for providing the sequence data for these assemblies, as well as the Sanger Institute for their collaborative work in sequencing the initial C. briggsae cb1 genome. Thanks also to the WormBase consortium for providing access to the cb1 sequence.

The worm sequences are made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. The centers producing the data reserve the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome.
  4. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects and the resulting NHGRI policy statement.
  5. Any redistribution of the data should carry this notice.


  Yeast Genome

UCSC Sacchromyces cerevisiae Genome Browser (sacCer3): Hiram Clawson, Greg Roe, Steve Heitner.
The April 2011 Sacchromyces cerevisiae genome assembly is based on sequence dated April 2011 in the Sacchromyces Genome Database (SGD). This genome sequence was downloaded from NCBI (genbank/genomes/Eukaryotes/fungi/Saccharomy ces_cerevisiae/SacCer_Apr2011/). The SGD™ gene annotations were downloaded from the SGD downloads site. The S288C strain was used in this sequencing project.

The June 2008 Sacchromyces cerevisiae genome assembly (sacCer2) is based on sequence dated June 2008 in the Sacchromyces Genome Database (SGD) and was obtained from the site http://downloads.yeastgenome.org/sequence/genomic_sequence/chromosomes/fasta/ The S288C strain was used in this sequencing project.

The Oct. 2003 Sacchromyces cerevisiae genome assembly (sacCer1) is based on sequence dated 1 Oct. 2003 in the Sacchromyces Genome Database (SGD). The sequence, open reading frame (ORF), and gene annotations were downloaded from the site http://www.yeastgenome.org/download-data/sequence. The cellular localization and protein abundance data displayed in the Gene Sorter are taken from the Yeast GFP Fusion Localization Database.

See the SGD Systematic Sequencing Table for credit and contact information for each of the chromosomes in the assembly. We'd like to thank Stanford University, the SGD, the University of California San Francisco (UCSF), Washington University in St. Louis, and The Broad Institute for providing the data and annotations for this release.


  California Sea Hare Genome

The Aplysia californica genome assembly has the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC California Sea Hare (aplCal1) Genome Browser: Galt Barber, Brian Raney, Hiram Clawson, Katrina Learned and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

The California sea hare sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.


  Ebola Virus Genome

The Ebola virus genome assembly has the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC Ebola virus (eboVir3) Genome Browser: Hiram Clawson, Brian Raney, Maximillian Haeussler, Angie Hirichs, Kate Rosenbloom, Chris Eisenhart, Pauline Fujita, Matthew Speir, Donna Karolchik, Ann Zweig, David Haussler, and Jim Kent
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA
Other Acknowledgements:

Thank you to Phillip Berman and his lab at UCSC for providing continued feedback on the Ebola virus Genome Browser, and to the Pardis Sabeti Lab at the Broad Institute for their guidance.

Thank you to the following institutions for proving additional annotations on the Ebola virus genome:

The Ebola virus sequence may be freely downloaded, used in analyses, and repackaged in databases. The data may be freely used in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.


  External Contributors to the UCSC Genome Browser Project

  Acknowledgment of Early Support

During the initial stage of this project, from January 2000 to June 2001, we received no direct federal funding to develop the working draft other than travel support. However, we gratefully acknowledge the support for our personnel provided by our basic bioinformatics research grants, especially DOE grant DE-FG03-99ER62849 (to develop gene-finding methods), but also NSF grant DBI-9809007, UC BIOTECH grant 99-11, a grant from the Sloan Foundation, the David and Lucille Packard Foundation, NIH grant GM-52848, and the Zahler grant that provided support for Jim Kent in the early stages of this work.

We are particularly thankful for the risks that Patrick Mantey (UCSC Dean of Engineering), James Gill (Vice Chancellor for Research), John Simpson (UCSC Provost), and M.R.C. Greenwood (UCSC Chancellor) were willing to take in advancing us the money in February 2000 needed to build the original 100-node LINUX cluster used in this work, and in the case of Dean Mantey, additional personnel support. Phokion Kolaitis, Chair of Computer Science, contributed as well.

We thank Compaq for providing an additional 100-CPU computational cluster in Cambridge, MA for use by the public human genome effort. We thank ILOG, Inc. (now part of IBM) for providing discounted licenses to its CPLEX linear programming software, which was essential for some of our early experiments.

In December 2000, HHMI began providing support for equipment and personnel. In the summer of 2001, HHMI provided the primary funding for a new cluster of 1000 CPUs running LINUX purchased from Rackable (now SGI), with additional support from CISI and NHGRI. Dubbed the UCSC KiloKluster, this equipment became the computational backbone for the initial years of the Genome Browser project.