Unit

UNIT 1.4 The UCSC Genome Browser

  1. Donna Karolchik,
  2. Angie S. Hinrichs,
  3. W. James Kent

Published Online: 1 MAR 2007

DOI: 10.1002/0471250953.bi0104s17

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Karolchik, D., Hinrichs, A. S. and Kent, W. J. 2007. The UCSC Genome Browser. Current Protocols in Bioinformatics. 17:1.4:1.4.1–1.4.24.

Author Information

  1. University of California Santa Cruz, Santa Cruz, California

Publication History

  1. Published Online: 1 MAR 2007
  2. Published Print: MAR 2007

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

Abstract

The University of California Santa Cruz (UCSC) Genome Browser (genome.ucsc.edu) 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—generated by the UCSC Genome Bioinformatics Group and external collaborators—display gene predictions, mRNA and expressed sequence tag alignments, simple nucleotide polymorphisms, expression and regulatory data, and pairwise and multiple-species comparative genomics data. All information relevant to a region is presented in one window, facilitating biological analysis and interpretation. The database tables underlying the Genome Browser tracks can be viewed, downloaded, and manipulated using another Web-based application, the UCSC Table Browser. Users can upload personal data as custom annotation tracks in both browsers for research or educational use. This unit describes how to use the Genome Browser and Table Browser for genome analysis, download the underlying database tables, and create and display custom annotation tracks.

Keywords:

  • Genome Browser;
  • Table Browser;
  • UCSC;
  • human genome;
  • genome analysis;
  • comparative genomics