[Bioperl-l] mismatch string search in BioPerl?

[Paul Gordon]

More generically, there is also String::Approx, which does much of the
same job. It has the trade off of not requiring EMBOSS, but having to
compile a binary object.

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Purgamentum init, exit purgamentum

Paul Gordon
Research Associate
University of Calgary

On Fri, 26 Apr 2002, Heikki Lehvaslaiho wrote:

> 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
> > >
> > >
> > >
> > >
> > 
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> -- 
> ______ _/      _/_____________________________________________________
>       _/      _/                      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
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