[Bioperl-l] BLAST and parsing question

[Marc Logghe]

Have you already looked into MUMmer ? I believe you even don't need a
sliding window approach. Given the complete query sequence, the
application will just show the stretches of exact matches.
It is based on suffix trees. Disadvantage however, is that currently
there is no possibility to store the indexes to the suffix trees, e.g.
you can not 'formatdb' your sequences into a 'MUMmer database'. The
suffix tree datastructures for the 'database' are generated in every run
and stored into memory.
Check it out at http://mummer.sourceforge.net/.
Cheers,
Marc


Marc Logghe, PhD
Expert Scientist Bioinformatics
deVGen NV
Technologiepark 30
B - 9052 Ghent-Zwijnaarde
Tel. +32 9 324 24 83 
Fax. +32 9 324 24 25 
Web: www.devgen.com

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> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Torsten Seemann
> Sent: Wednesday, April 26, 2006 1:57 AM
> To: Robert Murphy
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] BLAST and parsing question
> 
> On Tue, 2006-04-25 at 17:14 +0000, Robert Murphy wrote:
> > Question, is there a program that will search all my out files for 
> > just ones that have exact matches?  That might just slove 
> my problem.
> 
> The EMBOSS set of tools comes with a few options, perhaps 
> 'wordmatch' ?
> http://bioweb.pasteur.fr/docs/EMBOSS/wordmatch.html
> 
> --
> Torsten Seemann <torsten.seemann at infotech.monash.edu.au>
> Victorian Bioinformatics Consortium
> 
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