FrameDP: sensitive peptide detection on noisy matured sequences

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.