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Bioinformatics Advance Access originally published online on January 19, 2009
Bioinformatics 2009 25(5):670-671; doi:10.1093/bioinformatics/btp024
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

FrameDP: sensitive peptide detection on noisy matured sequences

Jérôme Gouzy 1, Sébastien Carrere 1 and Thomas Schiex 2,*

1Laboratoire Interactions Plantes Micro-organismes (LIPM) UMR441/2594, INRA/CNRS and 2Unité de Biométrie et d'Intelligence Artificielle UR 875, INRA, F-31320 Castanet Tolosan, France

*To whom correspondence should be addressed.


  Abstract

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.

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.

Contact: thomas.schiex{at}toulouse.inra.fr

Associate Editor: Alex Bateman

Received on October 22, 2008; revised on December 22, 2008; accepted on January 8, 2009

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