The USGC Genome Browser Database: 2008 Update


Authored by  D Karlochik*, RM Kuhn*, R Baertsch*, GP Barber*, H Clawson*, M Diekhans*, B Giardine *, RA Harte*, AS Hinrichs*, FS Hsu*, KM Kober *, W Miller E*, JS Pdersen*, A Pohl *, B Rhead *, KR Rosenbloom*, KE Smith*, M Stanke, A Thakkapallayil*, H Trumbower*, AS Zweig*, T Wang*, D Haussler*, WJ Kent*

Published in Nucleic Acids Research     
* This author is not affiliated with PMI.

Abstract

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/