{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,23]],"date-time":"2026-01-23T21:55:58Z","timestamp":1769205358524,"version":"3.49.0"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2813,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Transcriptome sequencing represents a fundamental source of information for genome-wide studies and transcriptome analysis and will become increasingly important for expression analysis as new sequencing technologies takes over array technology. The identification of the protein-coding region in transcript sequences is a prerequisite for systematic amino acid-level analysis and more specifically for domain identification. In this article, we present FrameDP, a self-training integrative pipeline for predicting CDS in transcripts which can adapt itself to different levels of sequence qualities.<\/jats:p>\n               <jats:p>Availability: FrameDP for Linux (web-server and underlying pipeline) is available at {{http:\/\/iant.toulouse.inra.fr\/FrameDP}} for direct use or a standalone installation.<\/jats:p>\n               <jats:p>Contact: \u00a0thomas.schiex@toulouse.inra.fr<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp024","type":"journal-article","created":{"date-parts":[[2009,1,20]],"date-time":"2009-01-20T01:44:58Z","timestamp":1232415898000},"page":"670-671","source":"Crossref","is-referenced-by-count":92,"title":["FrameDP: sensitive peptide detection on noisy matured sequences"],"prefix":"10.1093","volume":"25","author":[{"given":"J\u00e9r\u00f4me","family":"Gouzy","sequence":"first","affiliation":[{"name":"1 Laboratoire Interactions Plantes Micro-organismes (LIPM) UMR441\/2594, INRA\/CNRS and 2Unit\u00e9 de Biom\u00e9trie et d'Intelligence Artificielle UR 875, INRA, F-31320 Castanet Tolosan, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S\u00e9bastien","family":"Carrere","sequence":"additional","affiliation":[{"name":"1 Laboratoire Interactions Plantes Micro-organismes (LIPM) UMR441\/2594, INRA\/CNRS and 2Unit\u00e9 de Biom\u00e9trie et d'Intelligence Artificielle UR 875, INRA, F-31320 Castanet Tolosan, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Schiex","sequence":"additional","affiliation":[{"name":"1 Laboratoire Interactions Plantes Micro-organismes (LIPM) UMR441\/2594, INRA\/CNRS and 2Unit\u00e9 de Biom\u00e9trie et d'Intelligence Artificielle UR 875, INRA, F-31320 Castanet Tolosan, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,1,19]]},"reference":[{"key":"2023013110114103200_B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023013110114103200_B2","doi-asserted-by":"crossref","first-page":"900","DOI":"10.1093\/bioinformatics\/btl001","article-title":"REMORA: a pilot in the ocean of BioMoby web-services","volume":"22","author":"Carrere","year":"2006","journal-title":"Bioinformatics"},{"key":"2023013110114103200_B3","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/0167-9473(92)90042-E","article-title":"A classification EM algorithm for clustering and two stochastic versions","volume":"14","author":"Celeux","year":"1992","journal-title":"Comput. 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