[Bioperl-l] mismatch string search in BioPerl?

[Brian Osborne]

Martin,

>From the FAQ :

  2. How do I do motif searches with Bioperl? Can I do "find all sequences
     that are 75% identical" to a given motif?

     There are a number of approaches inside and outside of Bioperl. Within
     Bioperl take a look at Bio::Tools::SeqPattern, but it's also
conceivable
     that the combination of Bioperl and Perl's regular expressions could do
     the trick. You might also consider the CPAN module String::Approx (this
     module addresses the percent match query). Or, take a look at the TFBS
     package, at http://forkhead.cgb.ki.se/TFBS (Transcription Factor
Binding
     Site). This Bioperl-compliant package specializes in pattern searching
     of nucleotide sequence using matrices.


Brian O.

-----Original Message-----
From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
Behalf Of Martin Schenker
Sent: Thursday, April 25, 2002 1:03 PM
To: bioperl-l@bioperl.org
Subject: [Bioperl-l] mismatch string search in BioPerl?


Hi all!

Is there something like a mismatch string search as a module in BioPerl? I
try to find e.g. a 30 AA string (one mismatch allowed) in a sequence. I
could write some sledge-hammer code permuting happily through the string
with a "." on any possible position but perhaps someone had a
better/faster/neater idea already?!?

Thanks for any pointers!

Cheers, Martin

> Dr. Martin Schenker
> Bioinformatics/Software Eng.
> Oxford GlycoSciences (UK) Ltd
> The Forum
> 86 Milton Park
> Abingdon
> Oxon. OX14 4RY
> UK
>
> Tel: 	+44 (0)1235 208064
> Fax:	+44 (0)1235 208012
> Mobile:	+44 (0)7762 093310
> email:    mailto:Martin.Schenker@ogs.co.uk
> World-wide Web: http://www.ogs.com
>
>
>
>


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