- Genome Browser
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We have two MySQL databases for public access:
These servers allow 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 in summer, GMT -8:00 in winter).
You must have MySQL client libraries installed on your computer. We recommend using the most current version of the v5.0 MySQL clients.
You can connect to the US MySQL server using the command:
mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -P 3306
Or the European MySQl server with this command:
mysql --user=genome --host=genome-euro-mysql.soe.ucsc.edu -A -P 3306
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) if you would like to access the US public MySQL server:
#US MySQL server db.host=genome-mysql.soe.ucsc.edu db.user=genomep db.password=password central.db=hgcentral central.host=genome-mysql.soe.ucsc.edu central.user=genomep central.password=password gbdbLoc1=http://hgdownload.soe.ucsc.edu/gbdb/ forceTwoBit=on
Or these lines if you'd like to access the European MySQL server:
#European MySQL server db.host=genome-euro-mysql.soe.ucsc.edu db.user=genomep db.password=password central.db=hgcentral central.host=genome-euro-mysql.soe.ucsc.edu central.user=genomep central.password=password gbdbLoc1=http://hgdownload.soe.ucsc.edu/gbdb/ forceTwoBit=on
central.* settings tell our utilities how to connect to the public MySQL server.
gbdbLoc1 setting tells our utilities where to find data files.
forceTwoBit setting is necessary for utilities that retrieve genomic sequence.
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 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.