Re: [Transdecoder-users] Announcement: Transdecoder release r20140704

[Brian H. <bh...@br...>]

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