Fetch Data from UCSC Genome Browser

November 3, 2013   

Previously, I’ve shown that you can use a mysql database browser (e.g. Sequel Pro) to access and browse the UCSC Genome Browser MySQL database.

If you have a small dataset that you would like to annotate, you can write SQL statements to fetch data. Below I show how you can use python to fetch genome coordinates by specifying gene and genome build.

Note: The UCSC browser mysql resource will throttle you if you make too many queries. If you need to annotate large datasets, all of the data is freely available for download here.

Bioinformatics  Genetics  gist python