* 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
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
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
transdecoder is a dependency of trinityrnaseq. It will be team maintained by
myself and the Debian Med team.