FrameDP: sensitive peptide detection on noisy matured sequences

• Published in: Bioinformatics Vol. 25; no. 5; pp. 670 - 671
• Main Authors: Gouzy, Jérôme, Carrere, Sébastien, Schiex, Thomas
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.03.2009; Oxford Publishing Limited (England); Oxford University Press (OUP)
• Subjects: Applications Note; Bioinformatics; Biological and medical sciences; Computer Science; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling; General aspects; Internet; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Peptides - chemistry; Sequence Analysis, Protein - methods; Software; Peptides; Detection; FrameDP
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btp024

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@toulouse.inra.fr