Hi Careina,
There are several places on the web that describe the
PIR format (also called NBRF) E.g.
http://www.ebi.ac.uk/help/formats.html#pir
http://www.bioinformatics.nl/tools/crab_pir.html
etc.
The program readseq -- either via command line or
webserver -- e.g.
http://www.ebi.ac.uk/cgi-bin/readseq.cgi
http://iubio.bio.indiana.edu/cgi-bin/readseq.cgi
http://iubio.bio.indiana.edu/soft/molbio/readseq/java
can convert from many formats into PIR format (called
NBRF for output choice). Or you can convert from
fasta to pir pretty easy with a text editor if
it is just something you do occasionally.
However, since you mentioned that you wanted a pir format
file for use with arp/warp. I should mention that arp/warp
will only accept .pir files with a blank comment line
(i.e. the line after the 1st line (which starts >P1;)
must be blank rather than containing a free text
description of the sequence).
Regards,
Mitch
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Careina Edgooms
Sent: Thursday, February 17, 2011 9:57 PM
To: [log in to unmask]
Subject: [ccp4bb] .pir file
Dear CCP4 mailing list
I have a relatively simple question. How do I get sequence file in .pir format which is required for many programs? I normally use fasta format but some programs eg arpwarp do not allow me to use that
Thanks for your help
Careina
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