On 02/18/2011 07:42 AM, Vellieux Frederic wrote:
Arp Warp used to want a blank line between the > MALDH title, and the
first line of the sequence..
Not sure if that still holds.
Eleanor
a> Hi Careina,
Just an example of a pir file which I just generated (using Bart Hazes
program mcfman):
P1;>MALDH_
Just a title
TKVSVVGAAGTVGAAAGYNIALDIADEVVFVDIPDKEDDTVGQAADTNHGIAYDSNTRVR
QGGYEDTAGSDVVVITAGIPRQPGQTRIDLAGDNAPIMEDIQSSLDEHNDDYISLTTSNP
VDLLNRHLYEAGDRSREQVIGFGGRLDSARFRYVLSEEFDAPVQNVEGTILGEHGDAQVP
VFSKVSVDGTDPEFSGDEKEQLLGDLQESAMDVIERKGATEWGPARGVAHMVEAILHDTG
EVLPASVKLEGEFGHEDTAFGVPVSLGSNGVEEIVEWDLDDYEQDLMADAAEKLSDQYDK
IS*
I don't think the pir format has changed much since the subroutine that
extracts the sequence from a coordinate file was written. As you will
see the (ASCII) format is pretty simple, one start record, one title
record followed by records containing the sequence in the one-character
abbreviation, 60 characters per line, with "*" to end the sequence. The
start record is P1;> followed by 6 characters.
I never had any problems with the pir files generated by mcfman, and I
always have used an editor (vi is the one I use) to convert other
formats to this format.
Fred.
Careina Edgooms wrote:
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
