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The UCSC Genome Browser Database: update 2006
Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC) Santa Cruz, CA 95064, USA 1Howard Hughes Medical Institute, University of California Santa Cruz (UCSC) Santa Cruz, CA 95064, USA 2Institute for Genome Sciences and Policy, Duke University Durham, NC 27708, USA
*To whom correspondence should be addressed. Tel: +1 831 459 1544; Fax: +1 831 459 1809; Email: angie{at}soe.ucsc.edu
Received September 15, 2005. Revised October 27, 2005. Accepted October 27, 2005.
The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, mRNA and expressed sequence tag evidence, comparative genomics, regulation, expression and variation data. The database is optimized to support fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. The Genome Browser displays a wide variety of annotations at all scales from single nucleotide level up to a full chromosome. The Table Browser provides direct access to the database tables and sequence data, enabling complex queries on genome-wide datasets. The Proteome Browser graphically displays protein properties. The Gene Sorter allows filtering and comparison of genes by several metrics including expression data and several gene properties. BLAT and In Silico PCR search for sequences in entire genomes in seconds. These tools are highly integrated and provide many hyperlinks to other databases and websites. The GBD, browsing tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/.
Present address: C. W. Sugnet, Affymetrix Inc., Santa Clara, CA 95051, USA
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