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The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in <jats:italic>C. elegans<\/jats:italic>, and to apply this knowledge to the annotation of the genomes of four additional <jats:italic>Caenorhabditis<\/jats:italic> species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets across 10 Mb of the <jats:italic>C. elegans<\/jats:italic> genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>The most accurate gene-finders were 'combiner' algorithms, which made use of transcript- and protein-alignments and multi-genome alignments, as well as gene predictions from other gene-finders. Gene-finders that used alignments of ESTs, mRNAs and proteins came in second. There was a tie for third place between gene-finders that used multi-genome alignments and <jats:italic>ab initio<\/jats:italic> gene-finders. The median gene level sensitivity of combiners was 78% and their specificity was 42%, which is nearly the same accuracy reported for combiners in the human genome. <jats:italic>C. elegans<\/jats:italic> genes with exons of unusual hexamer content, as well as those with unusually many exons, short exons, long introns, a weak translation start signal, weak splice sites, or poorly conserved orthologs posed the greatest difficulty for gene-finders.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>This experiment establishes a baseline of gene prediction accuracy in <jats:italic>Caenorhabditis<\/jats:italic> genomes, and has guided the choice of gene-finders for the annotation of newly sequenced genomes of <jats:italic>Caenorhabditis<\/jats:italic> and other nematode species. We have created new gene sets for <jats:italic>C. briggsae<\/jats:italic>, <jats:italic>C. remanei<\/jats:italic>, <jats:italic>C. brenneri<\/jats:italic>, <jats:italic>C. japonica<\/jats:italic>, and <jats:italic>Brugia malayi<\/jats:italic> using some of the best-performing gene-finders.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-9-549","type":"journal-article","created":{"date-parts":[[2008,12,19]],"date-time":"2008-12-19T19:15:10Z","timestamp":1229714110000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":61,"title":["nGASP \u2013 the nematode genome annotation assessment project"],"prefix":"10.1186","volume":"9","author":[{"given":"Avril","family":"Coghlan","sequence":"first","affiliation":[]},{"given":"Tristan J","family":"Fiedler","sequence":"additional","affiliation":[]},{"given":"Sheldon J","family":"McKay","sequence":"additional","affiliation":[]},{"given":"Paul","family":"Flicek","sequence":"additional","affiliation":[]},{"given":"Todd W","family":"Harris","sequence":"additional","affiliation":[]},{"given":"Darin","family":"Blasiar","sequence":"additional","affiliation":[]},{"name":"the nGASP Consortium","sequence":"additional","affiliation":[]},{"given":"Lincoln D","family":"Stein","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2008,12,19]]},"reference":[{"issue":"5396","key":"2534_CR1","doi-asserted-by":"publisher","first-page":"2012","DOI":"10.1126\/science.282.5396.2012","volume":"282","author":"The C. elegans Sequencing Consortium","year":"1998","unstructured":"The C. elegans Sequencing Consortium: Genome sequence of the nematode C. elegans : a platform for investigating biology. 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