NAR Molecular Biology Database Collection entry number 316

http://genome.ucsc.edu/

Kuhn, R.M.¹, Karolchik, D.¹, Zweig, A.S.¹, Wang, T.¹, Smith, K.E.¹, Rosenbloom, K.R.¹, Rhead, B.¹, Raney, B.J.¹, Pohl, A.¹, Pheasant, M.¹, Meyer, L.¹, Hsu, F.¹, Hinrichs, A.S.¹, Harte, R.A.¹, Giardine, B.³, Fujita, P.¹, Diekhans, M.¹, Dreszer, T.¹, Clawson, H.¹, Barber1, G.P.^,, Haussler, D.^1,2, and Kent, W.J.¹

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

Contact genome@soe.ucsc.edu

The University of California Santa Cruz (UCSC) Genome Browser Database is an up-to-date source for genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. The database is optimized to support fast interactive performance with the UCSC Genome Browser, a web-based tool suite built on top of the database for rapid visualization, examination, and querying of the data at many levels. The Genome Browser Database, browsing tools, downloadable data files, and documentation can all be found on the UCSC Genome Bioinformatics web site.

New features of the UCSC database and Genome Browser viewer include:
*New genome assemblies to the database: initial assemblies for nine new organisms (orangutan, marmoset, guinea pig, zebra finch, lamprey, lancelet, and three Caenorhabditis species: brenneri, remanei, and japonica).
*Updated assemblies for the cow, zebrafish, sea urchin and C. elegans.
*Much new annotation data. Highlights: New UCSC Genes annotations; new variation data, including enhanced details pages for dbSNP data, new indel mapping and the HGSV Discordant track that maps clones from eight individuals from the HapMap Project to the reference assembly; Transmap, a homology-based mapping of mRNAs from other species onto many genomes; and a 30-vertebrate-alignment conservation track (multiz and phastCons) on the mm9 mouse assembly
*in silico-PCR results are now drawn as a browser track.
*BedGraph and MAF data types now available as custom tracks.
*Better longevity of custom tracks when saved in sessions.
*Online help
-online tutorial: http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml.
-help: http://genome.ucsc.edu/goldenpath/help
-FAQ: http://genome.ucsc.edu/FAQ
-mailing list help email: genome@soe.ucsc.edu

Major funding for the UCSC Genome Browser database project is via a P41 resource grant from NHGRI (1P41HG002371-08) with additional funding from the Howard Hughes Medical Institute.

Go to the abstract in the NAR 2009 Database Issue.

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