transdecoder longorfs

TransDecoder.LongOrfs Command

TransDecoder.LongOrfs Command

TransDecoder.LongOrfs

find coding regions within RNA transcript sequences

Maintainer: Debian Med Packaging Team



Section: science

Install TransDecoder.LongOrfs

  • Debian apt-get install transdecoder Click to copy
  • Ubuntu apt-get install transdecoder Click to copy
  • Kali Linux apt-get install transdecoder Click to copy
  • Raspbian apt-get install transdecoder Click to copy

transdecoder

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.

Installation of latest TransDecoder.LongOrfs command is available for Debian, Ubuntu, Kali and Raspbian. You can copy the command for your OS from above and paste it into your terminal. Once you run the command it will download the 2022 latest package from the repository and install it in your computer/server.