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Nucleic Acids Research Advance Access published online on November 7, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn875
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© 2008 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: update 2009

R. M. Kuhn1,*, D. Karolchik1, A. S. Zweig1, T. Wang1, K. E. Smith1, K. R. Rosenbloom1, B. Rhead1, B. J. Raney1, A. Pohl1, M. Pheasant1, L. Meyer1, F. Hsu1, A. S. Hinrichs1, R. A. Harte1, B. Giardine2, P. Fujita1, M. Diekhans1, T. Dreszer1, H. Clawson1, G. P. Barber1, D. Haussler1,3 and W. J. Kent1

1Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, 2Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and 3Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA

*To whom correspondence should be addressed. Tel: +1 831 459 1487; Fax: +1 831 459 1809; Email: kuhn{at}soe.ucsc.edu

Received September 12, 2008. Revised October 16, 2008. Accepted October 17, 2008.

The UCSC Genome Browser Database (GBD, http://genome.ucsc.edu) is a publicly available collection of genome assembly sequence data and integrated annotations for a large number of organisms, including extensive comparative-genomic resources. In the past year, 13 new genome assemblies have been added, including two important primate species, orangutan and marmoset, bringing the total to 46 assemblies for 24 different vertebrates and 39 assemblies for 22 different invertebrate animals. The GBD datasets may be viewed graphically with the UCSC Genome Browser, which uses a coordinate-based display system allowing users to juxtapose a wide variety of data. These data include all mRNAs from GenBank mapped to all organisms, RefSeq alignments, gene predictions, regulatory elements, gene expression data, repeats, SNPs and other variation data, as well as pairwise and multiple-genome alignments. A variety of other bioinformatics tools are also provided, including BLAT, the Table Browser, the Gene Sorter, the Proteome Browser, VisiGene and Genome Graphs.


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