Querying the UCSC database with a MySQL client

UCSC Genome Browser is founded and maintained by University of California Santa Cruz (UCSC), which contains genomic sketches and annotated information for several species, including humans, mice and rats, and provides a range of web analysis tools.

• 1.MySQL Installation

I am using the Centos6.8 system and we recommend Yum installation.

$ yum install-y MySQL mysql-devel mysql-server

• 2.MYSQLDB Installation

MYSQLDB is a thread-compatible interface for MySQL that provides the Python database API and recommends Yum installation.

$ yum install-y Mysql-python

• 3. Use the script geneinfo.py to get the bed information of the gene (note, the Genesymbol name)

$ python geneinfo.py BRCA1

"Reference list"

UCSC Database

UCSC database table Structure

Hgnc

Querying the UCSC database with a MySQL client