Package: wnpp
Severity: wishlist
* Package name : transdecoder
Version : 2.0.1
* 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.