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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.

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

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    Titre
    • The UCSC Genome Browser Database: 2008 update
    Auteur
    • Karolchik, D.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    • Kuhn, R. M.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    • Baertsch, R.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    • Barber, G. P.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    • Clawson, H.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    • Diekhans, M.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    • Giardine, B.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    • Harte, R. A.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    • Hinrichs, A. S.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    • Hsu, F.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    • Kober, K. M.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    • Miller, W.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    • Pedersen, J. S.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    • Pohl, A.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    • Raney, B. J.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    • Rhead, B.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    • Rosenbloom, K. R.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    • Smith, K. E.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    • Stanke, M.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    • Thakkapallayil, A.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    • Trumbower, H.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    • Wang, T.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    • Zweig, A. S.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    • Haussler, D.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    • Kent, W. J.. Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA, The Bioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark, Philip Morris International, Neuchatel, Switzerland, Navigenics, Inc., Redwood City, CA 94061, USA and Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
    Type de document
    • Postprint
    Langue
    • Anglais
    Publié dans
    • Nucleic Acids Research, 2008, vol. 36, p. D773-D779. Oxford University Press
    Autre version électronique
    Classification
    • Santé
    Mots clés
    Identifiant OAI-PMH
    • oai:doc.rero.ch:291818
    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