- Genome Browser
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We have a MySQL database for public access at genome-mysql.cse.ucsc.edu.
This server allows MySQL access to the same set of data currently available on our public Genome Browser site. The data are synchronized weekly with the main databases on our public site. During synchronization, the MySQL server can be intermittently out of sync with the main website for a short period of time. The weekly synchronization takes place on Monday mornings from 4:00 am to 9:00 am Pacific Time (GMT -7:00).
You must have MySQL client libraries installed on your computer. We recommend using the most current version of the v5.0 MySQL clients.
Connect to the MySQL server using the command:
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A
The -A flag is optional but is recommended for speed.
Once connected to the database, you may use a wide range of MySQL commands to query the database.
The MySQL database can also be used by the numerous utilities in the Genome Browser source tree. Some of these utilities require a password, so you will need to add the following specifications to your $HOME/.hg.conf file (remember to chmod your .hg.conf file to 600 permissions):
db.host=genome-mysql.cse.ucsc.edu db.user=genomep db.password=password central.db=hgcentral
If you prefer a graphical user interface (GUI) to the UCSC database tables, use the Table Browser.
System problems should be reported to firstname.lastname@example.org. Send questions regarding the database contents or queries to email@example.com. Messages sent to this address will be posted to the moderated genome mailing list, which is archived on a SEARCHABLE PUBLIC Google Groups forum.