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.
this package contains the documentation and sample data.