[Bioperl-l] regexp / protein database

Chris Fields cjfields at uiuc.edu
Tue Aug 29 12:00:39 EDT 2006


Funny, I was thinking along the lines of a motif search.  Didn't even think
of this solution!

Chris

> -----Original Message-----
> From: Cook, Malcolm [mailto:MEC at stowers-institute.org]
> Sent: Tuesday, August 29, 2006 10:43 AM
> To: Chris Fields; Hubert Prielinger
> Cc: bioperl-l at bioperl.org
> Subject: RE: [Bioperl-l] regexp / protein database
> 
> For swissprot, you might try SwissKnife
> (http://swissknife.sourceforge.net/docs/)
> 
> This will let you write something like this (based on example snippet
> provided):
> 
> 
> use SWISS::Entry;
> # Read an entire record at a time
> $/ = "\/\/\n";
> while (<>){
>   $entry = SWISS::Entry->fromText($_);
>   next unless $entry->SQs->seq =~ m/$YourRegExp/o;
>   DO WHAT YOU WANT TO THE SEQUENCE
> }
> 
> 
> 
> >-----Original Message-----
> >From: bioperl-l-bounces at lists.open-bio.org
> >[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
> >Sent: Monday, August 28, 2006 8:41 PM
> >To: Hubert Prielinger
> >Cc: bioperl-l at bioperl.org
> >Subject: Re: [Bioperl-l] regexp / protein database
> >
> >Hubert,
> >
> >This is answered in the FAQ.  You might also check the mail list
> >archives via gmane.
> >
> >http://www.bioperl.org/wiki/FAQ#Utilities
> >
> >http://search.gmane.org/?
> >query=&email=&group=gmane.comp.lang.perl.bio.general&sort=relev
> >ance&DEFA
> >ULTOP=and&query=
> >
> >Chris
> >
> >On Aug 28, 2006, at 8:15 PM, Hubert Prielinger wrote:
> >
> >> Hi,
> >> Is it possible to scan a protein database (e.g: swissprot..) directly
> >> with regular expression. I have taken a look at
> >> Bio::Tools::SeqPattern,
> >> but it seems it isn't a proper solution.
> >> like it is done on that webpage: http://scansite.mit.edu/
> >> dbsequence_reg.html
> >>
> >> thanks
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >Christopher Fields
> >Postdoctoral Researcher
> >Lab of Dr. Robert Switzer
> >Dept of Biochemistry
> >University of Illinois Urbana-Champaign
> >
> >
> >
> >_______________________________________________
> >Bioperl-l mailing list
> >Bioperl-l at lists.open-bio.org
> >http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >



More information about the Bioperl-l mailing list