Re: [Transdecoder-users] response to Kate

[Jahn D. <jah...@bi...>]

Dr Papanicolaou,
That did not work on my machine.
So after the
gunzip -c Pf*gz > Pfam-AB.hmm

I did,
hmmpress Pfam-AB.hmm

and proceeded to the 'hmmscan' call.

Should be OK? Not?


Jahn


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Fra: Ale...@cs... [mailto:Ale...@cs...]
Sendt: 21. desember 2013 03:18
Til: bh...@br...; tra...@li...
Emne: Re: [Transdecoder-users] response to Kate

Hello

It was downloaded the same day as the files were uploaded (17th of November 2013).

You can download the latest one
ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/
Pfam-A.hmm.gz
Pfam-B.hmm.gz
concatanate them and create a new binary version
gunzip -c Pf*gz > Pfam-AB.hmm
hmmconvert -b Pfam-AB.hmm > Pfam-AB.hmm.bin

place Pfam-AB.hmm.bin in /pfam (deleting any existing files) and run
make prep_pfam

i'll update the instructions for the next release
a

--
Dr. Alexie Papanicolaou

Phone: +61(0) 2 6246 4511| Mobile: +61 (0) 46 85 81 247
CSIRO Ecosystem Sciences, GPO Box 1700, Canberra 2601, ACT, Australia

-- CSIRO profile<http://www.csiro.au/Organisation-Structure/Divisions/Ecosystem-Sciences/AlexiePapanicolaou.aspx>
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-- Bioinformatics is also an experimental science
________________________________
From: Brian Haas [bh...@br...]
Sent: Saturday, 21 December 2013 9:10 AM
To: tra...@li...<mailto: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