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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.

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Running Instructions


Version 3.0.1