Re: [Transdecoder-users] Announcement: Transdecoder release r20140704
Extracting likely coding regions from transcript sequences
Brought to you by:
bhaas
From: Brian H. <bh...@br...> - 2015-01-09 17:12:55
|
ok - I can pretty much guarantee you that we're not going to see eye-to-eye on this, and we'll just have to agree to disagree. Alexie and I will do what we can, but it'll be what it is in the end and we're not planning to jump through hoops that we don't feel are essential or contradict how we (or I) feel about academic software. TransDecoder doesn't do any frameshift detection. You'd need some other process to correct errors before applying TransDecoder, as TransDecoder assumes that the sequence you're giving it is error-free. If you have a frameshift and that produces multiple ORFs that each look to have coding potential, and they meet the length requirement, then it'll report them as separate ORFs. Note, the TransDecoder algorithm is extremely simple and will produce many false positives as the length of the ORF decreases. If we end up properly addressing that issue, then I think the system would be worth publishing. If anyone has ideas - let's pursue it! Other than that, Pfam searches (and we'll include blastp or blastx searches in the next release) will yield improved sensitivity for those ORFs that are otherwise not meeting the coding metrics according to sequence composition. cheers, ~b |