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Bioinformatics. 2009 Mar 1;25(5):670-1. doi: 10.1093/bioinformatics/btp024. Epub 2009 Jan 19.

FrameDP: sensitive peptide detection on noisy matured sequences.

Author information

1
Laboratoire Interactions Plantes Micro-organismes (LIPM) UMR441/2594, INRA/CNRS, F-31320 Castanet Tolosan, France.

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.

PMID:
19153134
PMCID:
PMC2647831
DOI:
10.1093/bioinformatics/btp024
[Indexed for MEDLINE]
Free PMC Article

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