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Nucleic Acids Research Advance Access published online on December 17, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm966
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

The UCSC Genome Browser Database: 2008 update

D. Karolchik1,*, R. M. Kuhn1, R. Baertsch1, G. P. Barber1, H. Clawson1, M. Diekhans1, B. Giardine2, R. A. Harte1, A. S. Hinrichs1, F. Hsu1, K. M. Kober3, W. Miller2, J. S. Pedersen4, A. Pohl1, B. J. Raney1, B. Rhead1, K. R. Rosenbloom1, K. E. Smith1, M. Stanke5, A. Thakkapallayil1, H. Trumbower6, T. Wang1, A. S. Zweig1, D. Haussler7 and W. J. Kent1

1Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, 2Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, 3Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, 4The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, 5Philip Morris International, Neuchatel, Switzerland, 6Navigenics, Inc., Redwood City, CA 94061, USA and 7Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA

*To whom correspondence should be addressed. Tel: +1 831 459 1544; Fax: +1 831 459 1809; Email: donnak{at}soe.ucsc.edu

Received September 18, 2007. Revised October 17, 2007. Accepted October 17, 2007.

The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrate and 21 invertebrate species as of September 2007. For each assembly, the GBD contains a collection of annotation data aligned to the genomic sequence. Highlights of this year's additions include a 28-species human-based vertebrate conservation annotation, an enhanced UCSC Genes set, and more human variation, MGC, and ENCODE data. The database is optimized for fast interactive performance with a set of web-based tools that may be used to view, manipulate, filter and download the annotation data. New toolset features include the Genome Graphs tool for displaying genome-wide data sets, session saving and sharing, better custom track management, expanded Genome Browser configuration options and a Genome Browser wiki site. The downloadable GBD data, the companion Genome Browser toolset and links to documentation and related information can be found at: http://genome.ucsc.edu/.


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