Peer-Reviewed Publications

      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.
      Published
      Dec 17, 2007
      DOI
      10.1093/nar/gkm966
      PMID
      18086701
      Link to publication
      Topic
      Summary

      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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