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Methods and strategies for gene structure curation in WormBase.

The Caenorhabditis elegans genome sequence was published over a decade ago; this was the first published genome of a multi-cellular organism and now the WormBase project has had a decade of experience in curating this genome's sequence and gene structures. In one of its roles as a central repository for nematode biology, WormBase continues to refine the gene structure annotations using sequence similarity and other computational methods, as well as information from the literature- and community-submitted annotations. We describe the various methods of gene structure curation that have been tried by WormBase and the problems associated with each of them. We also describe the current strategy for gene structure curation, and introduce the WormBase 'curation tool', which integrates different data sources in order to identify new and correct gene structures. Database URL: http://www.wormbase.org/.

Pubmed ID: 21543339

Authors

  • Williams GW
  • Davis PA
  • Rogers AS
  • Bieri T
  • Ozersky P
  • Spieth J

Journal

Database : the journal of biological databases and curation

Publication Data

May 5, 2011

Associated Grants

  • Agency: Medical Research Council, Id: G0701197
  • Agency: NHGRI NIH HHS, Id: P41-HG02223

Mesh Terms

  • Animals
  • Base Sequence
  • Caenorhabditis elegans
  • Computational Biology
  • DNA, Intergenic
  • Databases, Genetic
  • Genes, Helminth
  • High-Throughput Nucleotide Sequencing
  • Molecular Sequence Annotation
  • Open Reading Frames