Re: [Transdecoder-users] response to Kate

[<Ale...@cs...>]

I'ts not really minimum length but an added option to keep long putative ORFs without any evidence for coding potential

If a protein is larger than the --retain_long_orfs, it will be reported regardless of lack of evidence (PFAM, hexamer score etc).
Anything with a PFAM score or other evidence but shorter than --retain_long_orfs, will be reported.

I've updated the USAGE help for the next release
thanks
a

________________________________
From: Brian Haas [bh...@br...]
Sent: Saturday, 21 December 2013 9:10 AM
To: tra...@li...
Cc: Papanicolaou, Alexie (CES, Black Mountain)
Subject: response to Kate

Hi Kate,

Alexie (CC'd) will be able to tell you for sure how old the provided version of pfam-AB is. I suspect it was from earlier this year.   You might want to just pull down the very latest version of the database, though, from the pfam website.

best,

~brian



Hi,

I am just wondering how old the provided Pfam AB database is? Using
Transdecoder +/- PFAM search with the provided AB dataset, I get very few
additional hits being included. If you don't think that getting the VERY
newest version should affect results greatly, I won't worry about it. My
organism is very non-model... P. falciparum malaria, so maybe PFAM
searching just isn't so great for my organism?

Also, am I correct that the minimum length cutoff is in effect no matter
what? I.e something with a PFAM score above noise but shorter than length
cutoff won't make the final list.

Thanks! And happiest holidays :) Kate

--
--
Brian J. Haas
The Broad Institute
http://broad.mit.edu/~bhaas