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Bug#778300: ITP: transdecoder -- find coding regions within transcripts

Package: wnpp
Severity: wishlist
Owner: Debian Med team <debian-med@lists.debian.org>
X-Debbugs-Cc: debian-devel@lists.debian.org, debian-med@lists.debian.org

* Package name    : transdecoder
  Version         : 2.0.1
  Upstream Author : Brian Haas <bhass@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
 TransDecoder identifies likely coding sequences based on the following
 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.

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