PSI-Blast

Arne Mueller a.mueller at icrf.icnet.uk
Tue Apr 27 16:46:31 EST 1999


armhold at topside.rutgers.edu wrote:
> 
> In article <3700C516.93CB62DD at icrf.icnet.uk>,
> 
> 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?
> 

Hi,

Thanks for that offer - but I just wrote my own parser ;-) (in python)
which looks for certain keywords in a psi-blast/blast file, hopefully
it'll survive the next blast version ... . They should add a blast
outputformat that's more machine readable, I mean witch certain fileds
for certain data. Blast output is/was intended to be readable for
humans, but I suppose nobody redas a 10MB psi-blast file ... ;-)

	greetings,

	Arne

-- 
Arne Mueller
Biomolecular Modelling Laboratory
Imperial Cancer Research Fund
44 Lincoln's Inn Fields
London WC2A 3PX, U.K.
phone : +44-(0)171 2693405      | Fax : +44-(0)171 269 3258
email : a.mueller at icrf.icnet.uk | http://www.icnet.uk/bmm/




More information about the Bio-soft mailing list