The UCSC Genome Browser

Curr Protoc Bioinformatics. 2009 Dec;Chapter 1:Unit1.4. doi: 10.1002/0471250953.bi0104s28.

Abstract

The University of California Santa Cruz (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-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, phenotype and variation 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 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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • California
  • Chromosome Mapping / methods*
  • Database Management Systems*
  • Databases, Genetic*
  • Information Storage and Retrieval / methods*
  • Internet*
  • Sequence Analysis, DNA / methods*
  • Software*
  • User-Computer Interface*