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Bioinformatics Advance Access published online on January 19, 2009
Bioinformatics, 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,*

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

*To whom correspondence should be addressed. Mr. Thomas Schiex, E-mail: Thomas.tschiex{at}toulouse.inra.fr


  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 paper, we present FrameDP, a self training integrative pipeline for predicting CDS in transcripts which can adapt itself to different levels of sequence qualities.

Contact: Thomas.Schiex{at}toulouse.inra.fr

Availability: FrameDP for Linux (web-server and underlying pipe-line) is available at {{http://iant.toulouse.inra.fr/FrameDP}} for direct use or a standalone installation.

Associate Editor: Dr. Alex Bateman

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

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