The UCSC Genome Browser
Open Access
- 15 March 2007
- journal article
- unit
- Published by Wiley in Current Protocols in Bioinformatics
- Vol. 17 (1), 1.4.1-1.4.24
- https://doi.org/10.1002/0471250953.bi0104s17
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
This publication has 38 references indexed in Scilit:
- Pfam: clans, web tools and servicesNucleic Acids Research, 2006
- A haplotype map of the human genomeNature, 2005
- NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteinsNucleic Acids Research, 2004
- The UCSC Table Browser data retrieval toolNucleic Acids Research, 2004
- The International HapMap ProjectNature, 2003
- The UCSC Genome Browser DatabaseNucleic Acids Research, 2003
- Initial sequencing and comparative analysis of the mouse genomeNature, 2002
- The Human Genome Browser at UCSCGenome Research, 2002
- BLAT—The BLAST-Like Alignment ToolGenome Research, 2002
- Integration of cytogenetic landmarks into the draft sequence of the human genomeNature, 2001