Accessing the UCSC Genome Browser MySQL Database

November 2, 2013   

The UCSC Genome browser has a publicly available MySQL database. There are a lot of different ways you can use it, including:

  • Annotating a small dataset
  • Understanding how data is formatted, and can be used.
  • Browsing Data

If you are on a mac – Sequel Pro is a fantastic tool for browsing.

Connecting

To browse the UCSC genome browser database, download Sequal Pro and enter in the following connection information into the login screen:

UCSC MySQL

You should be presented with a screen that looks like this:

Browsing UCSC Genome MySQL database

Databases are represented as Connection/Resource > Database > Tables > Rows. Sequal pro lets you connect to the UCSC Browser MySQL server. Each database represents a different genome. Remember that genomes change and improve over time – so there are multiple builds of each genome (e.g. hg18 and hg19) represented by separate databases.

Within each database are tables. These are the same tables referred to on the UCSC website – and you can find out more about what the data represents on the browser website by clicking ‘describe table schema’ for the table of interest as shown below.

Bioinformatics  Genetics