[Transdecoder-users] response to Kate

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

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