Package: wnpp Severity: wishlist Owner: Debian Med team <debian-...@lists.debian.org> X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org
* Package name : transdecoder Version : 2.0.1 Upstream Author : Brian Haas <bh...@broadinstitute.org> * URL : http://transdecoder.github.io/ * License : BSD-3-clause Programming Lang: Perl Description : find coding regions within transcripts TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. . TransDecoder identifies likely coding sequences based on the following criteria: . a minimum length open reading frame (ORF) is found in a transcript sequence . a log-likelihood score similar to what is computed by the GeneID software is > 0. . the above coding score is greatest when the ORF is scored in the 1st reading frame as compared to scores in the other 5 reading frames. . if a candidate ORF is found fully encapsulated by the coordinates of another candidate ORF, the longer one is reported. However, a single transcript can report multiple ORFs (allowing for operons, chimeras, etc). . optional the putative peptide has a match to a Pfam domain above the noise cutoff score. transdecoder is a dependency of trinityrnaseq. It will be team maintained by myself and the Debian Med team.