find coding regions within RNA transcript sequences

 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.