Package: transdecoder (5.0.1-1)

Links for transdecoder

Trisquel Resources:

Download Source Package transdecoder:

Maintainer:

Debian Med Packaging Team (Mail Archive)

Original Maintainers:

Debian Med Packaging Team (Mail Archive)
Michael R. Crusoe
Andreas Tille

External Resources:

Homepage [transdecoder.github.io]

Similar packages:

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.

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