The UCSC Genome Browser Database: 2008 update

Karolchik, D.
Kuhn, R. M.
Baertsch, R.
Barber, G. P.
Clawson, H.
Diekhans, M.
Giardine, B.
Harte, R. A.
Hinrichs, A. S.
Hsu, F.
Kober, K. M.
Miller, W.
Pedersen, J. S.
Pohl, A.
Raney, B. J.
Rhead, B.
Rosenbloom, K. R.
Smith, K. E.
Stanke, M.
Thakkapallayil, A.
Trumbower, H.
Wang, T.
Zweig, A. S.
Haussler, D.
Kent, W. J.

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
⁷Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA

Received September 18, 2007; Revised and Accepted October 17, 2007

^*To whom correspondence should be addressed. Tel: +1 831 459 1544; Fax: +1 831 459 1809; Email: [email protected]

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.

Nucleic Acids Research 36:p D773-D779, January 2008.

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/.