Is it possible to run SQL queries directly on the database rather than using the Table Browser interface?
Response: In response to requests from Genome Browser users, we have set up a MySQL database for public access at genome-mysql.cse.ucsc.edu. This new server allows MySQL access to the same set of data currently available on our public Genome Browser site. The data are synchronized daily with the main databases on http://genome.ucsc.edu. To connect to the database, you must use a computer on which the MySQL client libraries have been installed. The UCSC server is running MySQL 5.0.67; for best results, we recommend you use clients of the same revision. The v5.0 MySQL clients may be downloaded from http://dev.mysql.com/downloads/mysql/5.0.html.