TransDecoder.LongOrfs
find coding regions within RNA transcript sequences
Install
- All systems
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curl cmd.cat/TransDecoder.LongOrfs.sh
- Debian
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apt-get install transdecoder - Ubuntu
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apt-get install transdecoder - Kali Linux
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apt-get install transdecoder - Windows (WSL2)
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sudo apt-get updatesudo apt-get install transdecoder - Raspbian
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apt-get install transdecoder - Dockerfile
- dockerfile.run/TransDecoder.LongOrfs
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.