{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T12:21:58Z","timestamp":1784809318871,"version":"3.55.0"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: It is now easy and increasingly usual to produce oriented RNA-Seq data as a prokaryotic genome is being sequenced. However, this information is usually just used for expression quantification. EuGene-PP is a fully automated pipeline for structural annotation of prokaryotic genomes integrating protein similarities, statistical information and any oriented expression information (RNA-Seq or tiling arrays) through a variety of file formats to produce a qualitatively enriched annotation including coding regions but also (possibly antisense) non-coding genes and transcription start sites.<\/jats:p>\n               <jats:p>Availability and implementation: EuGene-PP is an open-source software based on EuGene-P integrating a Galaxy configuration. EuGene-PP can be downloaded at eugene.toulouse.inra.fr.<\/jats:p>\n               <jats:p>Contact: \u00a0erika.sallet@toulouse.inra.fr<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu366","type":"journal-article","created":{"date-parts":[[2014,6,1]],"date-time":"2014-06-01T00:10:10Z","timestamp":1401581410000},"page":"2659-2661","source":"Crossref","is-referenced-by-count":30,"title":["EuGene-PP: a next-generation automated annotation pipeline for prokaryotic genomes"],"prefix":"10.1093","volume":"30","author":[{"given":"Erika","family":"Sallet","sequence":"first","affiliation":[{"name":"1 Laboratoire Interactions Plantes Micro-organismes (LIPM) UMR441\/2594, INRA\/CNRS, F-31320 and 2 INRA, Unit\u00e9 de Math\u00e9matiques et Informatique Appliques de Toulouse, UR 875, Castanet-Tolosan F-31326, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00e9r\u00f4me","family":"Gouzy","sequence":"additional","affiliation":[{"name":"1 Laboratoire Interactions Plantes Micro-organismes (LIPM) UMR441\/2594, INRA\/CNRS, F-31320 and 2 INRA, Unit\u00e9 de Math\u00e9matiques et Informatique Appliques de Toulouse, UR 875, Castanet-Tolosan F-31326, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Schiex","sequence":"additional","affiliation":[{"name":"1 Laboratoire Interactions Plantes Micro-organismes (LIPM) UMR441\/2594, INRA\/CNRS, F-31320 and 2 INRA, Unit\u00e9 de Math\u00e9matiques et Informatique Appliques de Toulouse, UR 875, Castanet-Tolosan F-31326, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,5,30]]},"reference":[{"key":"2023012711554362800_btu366-B1","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1093\/bioinformatics\/btm009","article-title":"Identifying bacterial genes and endosymbiont DNA with Glimmer","volume":"23","author":"Delcher","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012711554362800_btu366-B2","doi-asserted-by":"crossref","first-page":"87","DOI":"10.2174\/157489308784340702","article-title":"Genome annotation in plants and fungi: EuGene as a model platform","volume":"3","author":"Foissac","year":"2008","journal-title":"Curr. 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