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 2 forward 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). + a PSSM is built/trained/used to refine the start codon prediction. + optional the putative peptide has a match to a Pfam domain above the noise cutoff score.

Please visit https://github.com/TransDecoder/TransDecoder/wiki for full documentation.

Releases can be downloaded from https://github.com/TransDecoder/TransDecoder/releases

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 2 forward 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). + a PSSM is built/trained/used to refine the start codon prediction. + optional the putative peptide has a match to a Pfam domain above the noise cutoff score. Please visit https://github.com/TransDecoder/TransDecoder/wiki for full documentation. Releases can be downloaded from https://github.com/TransDecoder/TransDecoder/releases