[Bioperl-l] mismatch string search in BioPerl?

[Lincoln Stein]

But be careful with String::Approx.  Its distance estimates are completely 
screwed up so you can't really control how many 
mismatches/insertions/deletions to accept.  It's far better (and faster) to 
pipe through agrep.

Lincoln

On Friday 26 April 2002 11:33, Paul Gordon wrote:
> 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.
>
> ----------------------------------------------------
> 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
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