[Bioperl-l] regexp / protein database

Cook, Malcolm MEC at stowers-institute.org
Tue Aug 29 11:43:17 EDT 2006


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
>
>
>
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>Bioperl-l at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



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