Transdecoder

Z MetaCentrum
Přejít na: navigace, hledání

Description

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.

Availability

version 3.0.1

Use

module add transdecoder-3.0.1

This makes available the path to the program binaries.

Documentation

http://transdecoder.github.io/

Licence

For more information see https://github.com/TransDecoder/TransDecoder/blob/master/LICENSE.txt

Program manager

meta@cesnet.cz

Homepage

http://transdecoder.github.io/