Erika Sallet1, Jérôme Gouzy1, Thomas Schiex1. 1. 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.
Abstract
UNLABELLED: 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. 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.
UNLABELLED: 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. 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.
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