title: EuGene-PP: a next-generation automated annotation pipeline for prokaryotic genomes.
abstract: 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.
  
  
  METHODS
  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.
authors.affiliation: Laboratoire Interactions Plantes Micro-organismes (LIPM) UMR441/2594, INRA/CNRS, F-31320 and INRA, Unité de Mathématiques et Informatique Appliques de Toulouse, UR 875, Castanet-Tolosan F-31326, France.
authors.forename: Erika
authors.initials: E
authors.lastname: Sallet
authors.affiliation: Laboratoire Interactions Plantes Micro-organismes (LIPM) UMR441/2594, INRA/CNRS, F-31320 and INRA, Unité de Mathématiques et Informatique Appliques de Toulouse, UR 875, Castanet-Tolosan F-31326, France.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Gouzy
authors.affiliation: Laboratoire Interactions Plantes Micro-organismes (LIPM) UMR441/2594, INRA/CNRS, F-31320 and INRA, Unité de Mathématiques et Informatique Appliques de Toulouse, UR 875, Castanet-Tolosan F-31326, France.
authors.forename: Thomas
authors.initials: T
authors.lastname: Schiex
mesh_terms: D001331:Automation; D001419:Bacteria / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D058977:Molecular Sequence Annotation / Q000379:methods*; D017423:Sequence Analysis, RNA; D012984:Software; D024363:Transcription Initiation Site