TransDecoder

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.

It uses 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.
*    start codon positions are refined according to a start-codon position weight matrix based feature scoring.


Full documentation is provided at: http://transdecoder.github.io




