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Nucleic Acids Research 2006 34(Database Issue):D590-D598; doi:10.1093/nar/gkj144
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Nucleic Acids Research, 2006, Vol. 34, Database issue D590-D598
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

The UCSC Genome Browser Database: update 2006

A. S. Hinrichs*, D. Karolchik, R. Baertsch, G. P. Barber, G. Bejerano, H. Clawson, M. Diekhans, T. S. Furey2, R. A. Harte, F. Hsu, J. Hillman-Jackson, R. M. Kuhn, J. S. Pedersen, A. Pohl, B. J. Raney, K. R. Rosenbloom, A. Siepel, K. E. Smith, C. W. Sugnet, A. Sultan-Qurraie, D. J. Thomas, H. Trumbower, R. J. Weber, M. Weirauch, A. S. Zweig, D. Haussler1 and W. J. Kent

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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