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. 2012 Jan 1;1(1):15-21.
doi: 10.4161/worm.19574.

WormBase: Annotating many nematode genomes

Kevin Howe  1 , Paul Davis, Michael Paulini, Mary Ann Tuli, Gary Williams, Karen Yook, Richard Durbin, Paul Kersey, Paul W Sternberg
Affiliations

WormBase: Annotating many nematode genomes

Kevin Howe et al. Worm. .

Abstract

WormBase (www.wormbase.org) has been serving the scientific community for over 11 years as the central repository for genomic and genetic information for the soil nematode Caenorhabditis elegans. The resource has evolved from its beginnings as a database housing the genomic sequence and genetic and physical maps of a single species, and now represents the breadth and diversity of nematode research, currently serving genome sequence and annotation for around 20 nematodes. In this article, we focus on WormBase's role of genome sequence annotation, describing how we annotate and integrate data from a growing collection of nematode species and strains. We also review our approaches to sequence curation, and discuss the impact on annotation quality of large functional genomics projects such as modENCODE.

Keywords: Caenorhabditis elegans; annotation; community resource; genome; model organism database; nematode; parasitic nematode; sequence curation.

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References

    1. Yook K, Harris TW, Bieri T, Cabunoc A, Chan J, Chen WJ, et al. WormBase 2012: more genomes, more data, new website. Nucleic Acids Res. 2012;40(Database issue):D735–41. doi: 10.1093/nar/gkr954. - DOI - PMC - PubMed
    1. Harris TW, Antoshechkin I, Bieri T, Blasiar D, Chan J, Chen WJ, et al. WormBase: a comprehensive resource for nematode research. Nucleic Acids Res. 2010;38(Database issue):D463–7. doi: 10.1093/nar/gkp952. - DOI - PMC - PubMed
    1. Mitreva M, Jasmer DP, Zarlenga DS, Wang Z, Abubucker S, Martin J, et al. The draft genome of the parasitic nematode Trichinella spiralis. Nat Genet. 2011;43:228–35. doi: 10.1038/ng.769. - DOI - PMC - PubMed
    1. Jex AR, Liu S, Li B, Young ND, Hall RS, Li Y, et al. Ascaris suum draft genome. Nature. 2011;479:529–33. doi: 10.1038/nature10553. - DOI - PubMed
    1. Kikuchi T, Cotton JA, Dalzell JJ, Hasegawa K, Kanzaki N, McVeigh P, et al. Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. PLoS Pathog. 2011;7:e1002219. doi: 10.1371/journal.ppat.1002219. - DOI - PMC - PubMed

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