UNIT 1.4 The UCSC Genome Browser

  1. Donna Karolchik,
  2. W. James Kent

Published Online: 1 FEB 2003

DOI: 10.1002/0471250953.bi0104s00

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Karolchik, D. and Kent, W. J. 2003. The UCSC Genome Browser. Current Protocols in Bioinformatics. 1:1.4.

Author Information

  1. University of California, Santa Cruz, California

Publication History

  1. Published Online: 1 FEB 2003
  2. Published Print: JAN 2003

This is not the most recent version of the article. View current version (1 DEC 2012)


The UCSC Genome Browser is a popular Web-based tool for quickly displaying a requested portion of a genome at any scale, accompanied by a series of aligned annotation tracks. The annotations - some of which are generated at the University of California, Santa Cruz (UCSC) and some by external collaborators - display gene predictions, mRNA alignments, expressed sequence tag alignments, cross-species homologies, single nucleotide polymorphisms, and several other types of data. All information relevant to a region is presented in one window, facilitating biological analysis and interpretation. Users can also upload custom annotation tracks for research or educational use. This unit describes how to use and customize the UCSC Genome Browser, download the underlying database tables, and create and display custom annotation tracks.