[Bioperl-l] Fuzzy matching sequences

[Paul Gordon]

Though you might run into the problem that blast won't necessarily
pickup all of the nmers, those they are short and the variations occur in
one or both index words...

________________________________________________________________________
Paul Gordon                                     Paul.Gordon@nrc.ca
Genomic Technologies				http://maggie.cbr.nrc.ca
Institute for Marine Biosciences
National Research Council Canada

On Fri, 16 Mar 2001, Brad Langhorst wrote:

> On Friday 16 March 2001 05:31 am, Kris Boulez wrote:
> > Do people know of a way to do this using perl regexes (I couldn't find
> > anything in the Friedl book). The only solution I can think of is to
> > create a blastable DB from the x-mers and blast all sequences against
> > this DB.
> I blased the x-mers against the sequence, it worked well
> and scaled very nicely on a time-logic blast host.
> I'm not sure how it would scale on normal hardware, probably just fine.
> 
> brad
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