Downloading Data using MySQL
We have a MySQL database for public access at genome-mysql.soe.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
Connect to the MySQL server using the command:
mysql --user=genome --host=genome-mysql.soe.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.
Conditions of use
Avoid excessive or heavy queries that may impact the server performance. Inappropriate query use
will result in a restriction of access. If you plan to execute a query that you think may be
excessive, contact UCSC first to avoid the possibility of having your access blocked.
Bot access and excessive program-driven use are not permitted.
Attachments by local mirror sites are prohibited.
Using the MySQL server with our utilities
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
If you have set up your .hg.conf file as above, you can use the
available from our downloads server in the
to access the public MySQL server. The benefit of using the
hgsql command is that
you don't have to include the username or password as part of your command. You only need to
specify the host:
hgsql -h genome-mysql.soe.ucsc.edu
If you prefer a graphical user interface (GUI) to the UCSC database tables, use the
System problems should be reported to
Send questions regarding the database contents or queries to
Messages sent to this address will be posted to the moderated genome mailing list, which is
archived on a SEARCHABLE, PUBLIC