{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T12:46:11Z","timestamp":1722689171089},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Gene models from draft genome assemblies of metazoan species are often incorrect, missing exons or entire genes, particularly for large gene families. Consequently, labour-intensive manual curation is often necessary. We present Figmop (Finding Genes using Motif Patterns) to help with the manual curation of gene families in draft genome assemblies. The program uses a pattern of short sequence motifs to identify putative genes directly from the genome sequence. Using a large gene family as a test case, Figmop was found to be more sensitive and specific than a BLAST-based approach. The visualization used allows the validation of potential genes to be carried out quickly and easily, saving hours if not days from an analysis.<\/jats:p>\n               <jats:p>Availability and implementation: Source code of Figmop is freely available for download at https:\/\/github.com\/dave-the-scientist , implemented in C and Python and is supported on Linux, Unix and MacOSX.<\/jats:p>\n               <jats:p>Contact: \u00a0curran.dave.m@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu544","type":"journal-article","created":{"date-parts":[[2014,8,13]],"date-time":"2014-08-13T13:59:18Z","timestamp":1407938358000},"page":"3266-3267","source":"Crossref","is-referenced-by-count":6,"title":["Figmop: a profile HMM to identify genes and bypass troublesome gene models in draft genomes"],"prefix":"10.1093","volume":"30","author":[{"given":"David M.","family":"Curran","sequence":"first","affiliation":[{"name":"1 Department of Ecosystem and Public Health and 2 Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, T2N 4Z6, Canada"},{"name":"1 Department of Ecosystem and Public Health and 2 Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, T2N 4Z6, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John S.","family":"Gilleard","sequence":"additional","affiliation":[{"name":"1 Department of Ecosystem and Public Health and 2 Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, T2N 4Z6, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James D.","family":"Wasmuth","sequence":"additional","affiliation":[{"name":"1 Department of Ecosystem and Public Health and 2 Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, T2N 4Z6, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,8,12]]},"reference":[{"key":"2023012712002464600_btu544-B1","doi-asserted-by":"crossref","first-page":"W369","DOI":"10.1093\/nar\/gkl198","article-title":"MEME: discovering and analyzing DNA and protein sequence motifs","volume":"34","author":"Bailey","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012712002464600_btu544-B2","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023012712002464600_btu544-B3","doi-asserted-by":"crossref","first-page":"R88","DOI":"10.1186\/gb-2013-14-8-r88","article-title":"The genome and transcriptome of \n              Haemonchus contortus\n              , a key model parasite for drug and vaccine discovery","volume":"14","author":"Laing","year":"2013","journal-title":"Genome Biol."},{"key":"2023012712002464600_btu544-B4","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1007\/978-1-60327-241-4_16","article-title":"Computational methods for \n              ab initio\n               and comparative gene finding","volume":"609","author":"Picardi","year":"2010","journal-title":"Methods Mol. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/22\/3266\/48931163\/bioinformatics_30_22_3266.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/22\/3266\/48931163\/bioinformatics_30_22_3266.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T12:29:38Z","timestamp":1674822578000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/22\/3266\/2391341"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,8,12]]},"references-count":4,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2014,11,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu544","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,11,15]]},"published":{"date-parts":[[2014,8,12]]}}}