PSI-Blast

armhold at topside.rutgers.edu armhold at topside.rutgers.edu
Thu Apr 15 14:02:36 EST 1999


In article <3700C516.93CB62DD at icrf.icnet.uk>,

> I'm looking for a tool to post process psi-blast output files. I run
> psi-blast to search in nrprot but I'm only interested in certain hits
> like 'pdb: ...'. I'd like to filter all these hits from ALL cycles of
> the psi-blast output. I havn't yet managed to do the job with mview ...
> so if you've an idea about a program that is able to filter psi-blast
> output in the may I described I'd be lucky to hear/read from you,

I wrote some short PERL code for parsing PSI-BLAST output for one of
our applications.  It's fairly tailored to our project, but if you can
grok PERL you can probably figure out how to tailor it to your needs.
Mail me if you want a copy.

PS: Is anyone else bothered by the BLAST docs mentioning that the output
is supposed to be non-parseble?

--
George Armhold                    PGP Key: [02D2EBE5]
Rutgers University            Fingerprint: [51 8B A4 B0 7A 71 7C E7]
Bioinformatics Initiative                  [85 DE 13 99 0B 68 5F 92]

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