The UCSC Genome Browser

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 exter...

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Bibliographic Details
Published inCurrent protocols in bioinformatics Vol. Chapter 1; p. 1.4.1
Main Authors Karolchik, Donna, Hinrichs, Angie S, Kent, W James
Format Journal Article
LanguageEnglish
Published United States 01.12.2012
Subjects
Databases, Genetic
Genome
Genomics - methods
Internet
Phenotype
RNA, Messenger - chemistry
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Summary: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 include 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 personal datasets in a wide variety of formats as custom annotation tracks in both browsers for research or educational purposes. 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.
ISSN:1934-340X
DOI:10.1002/0471250953.bi0104s40