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. 2006 Jan 1;34(Database issue):D475-8.
doi: 10.1093/nar/gkj061.

WormBase: better software, richer content

Erich M Schwarz  1 , Igor Antoshechkin, Carol Bastiani, Tamberlyn Bieri, Darin Blasiar, Payan Canaran, Juancarlos Chan, Nansheng Chen, Wen J Chen, Paul Davis, Tristan J Fiedler, Lisa Girard, Todd W Harris, Eimear E Kenny, Ranjana Kishore, Dan Lawson, Raymond Lee, Hans-Michael Müller, Cecilia Nakamura, Phil Ozersky, Andrei Petcherski, Anthony Rogers, Will Spooner, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Richard Durbin, John Spieth, Lincoln D Stein, Paul W Sternberg
Affiliations

WormBase: better software, richer content

Erich M Schwarz et al. Nucleic Acids Res. .

Abstract

WormBase (http://wormbase.org), the public database for genomics and biology of Caenorhabditis elegans, has been restructured for stronger performance and expanded for richer biological content. Performance was improved by accelerating the loading of central data pages such as the omnibus Gene page, by rationalizing internal data structures and software for greater portability, and by making the Genome Browser highly customizable in how it views and exports genomic subsequences. Arbitrarily complex, user-specified queries are now possible through Textpresso (for all available literature) and through WormMart (for most genomic data). Biological content was enriched by reconciling all available cDNA and expressed sequence tag data with gene predictions, clarifying single nucleotide polymorphism and RNAi sites, and summarizing known functions for most genes studied in this organism.

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References

    1. Eeckman F.H., Durbin R. ACeDB and macace. Methods Cell Biol. 1995;48:583–605. - PubMed
    1. Stein L.D., Thierry-Mieg J. Scriptable access to the Caenorhabditis elegans genome sequence and other ACEDB databases. Genome Res. 1998;8:1308–1315. - PMC - PubMed
    1. Chen N., Harris T.W., Antoshechkin I., Bastiani C., Bieri T., Blasiar D., Bradnam K., Canaran P., Chan J., Chen C.K., et al. WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Nucleic Acids Res. 2005;33:D383–D389. - PMC - PubMed
    1. Chen N., Lawson D., Bradnam K., Harris T.W., Stein L.D. WormBase as an integrated platform for the C.elegans ORFeome. Genome Res. 2004;14:2155–2161. - PMC - PubMed
    1. Stein L.D., Bao Z., Blasiar D., Blumenthal T., Brent M.R., Chen N., Chinwalla A., Clarke L., Clee C., Coghlan A., et al. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol. 2003;1:E45. - PMC - PubMed

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