[Bioperl-l] mismatch string search in BioPerl?

[Heikki Lehvaslaiho]

Martin,

Doing searches is a CPU intensive job most of the time, so consider using a
compiled program with a perl wrapper around it. 

See e.g. fuzzprot program in the EMBOSS package. We already have a generic
wrapper around EMBOSS, you'd only need to worry about processing the output.

	-Heikki


Martin Schenker wrote:
> 
> 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
> >
> >
> >
> >
> 
> **********************************************************************
> The information transmitted by this email is private and
> confidential and is intended for the use of the intended
> recipients specified therein.
> If you are neither an intended recipient nor an employee
> or agent responsible for delivery to an intended recipient,
> you should be aware that any dissemination, distribution
> or copying of this communication is strictly prohibited.
> If you received this communication in error, please
> notify us immediately.
> **********************************************************************
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________