[Bioperl-l] Findpatterns

[Jason Stajich]

See EMBOSS, http://www.emboss.org

The programs fuzznuc and dreg should accomplish what you want in terms of
pattern searching.

Jason Stajich
Duke University
jason at cgt.mc.duke.edu

On Sun, 24 Nov 2002, Fernandez-Capetillo, Oscar (NIH/NCI) wrote:

>
> Hi there,
> Not sure I need the Bio part of Perl to do this. Anyway, maybe somebody has
> tried this before and can help me out.
> I am trying to run the search of a short nucleotide pattern against the
> human and mouse genome databases. Exactly, I will want to find where a
> nucleotide pattern is present in the genome. My nucleotide pattern is of
> medium complexity (I can only represent it as a regular expression otherways
> the combinatios will be huge). Lets say something like:
> ACTCTATCANNNNNNNNNNNNNNACTATCTTGGCATCGACNNNNNNNNCATGCTAGCATCGGG
> I know that years ago the freely usable GCG package had a tool named
> findpatterns which you could use to do so. Unfortunately, people is not only
> driven by the shake of Science and now GCG is commercial (I wonder what will
> happen if Newton would have pattented the differential calculus). So I am
> all alone. I could try a Blast for short sequences, but it does not accept
> vaguities as NNNNN...
> I'd want to run it against both mouse and human genome databases, which I
> don't think I can access through the bioperl interface.
> I'd appreciate any help.Thanks,
> Oskar
> Oskar Fernandez-Capetillo, Ph. D.
>  NCI Build., 10 Room 4A01
> National Institute of Health
> 10 Center Drive
> Bethesda, MD
> 20892, 1360
>
> Phone: 301-496-4673
> Fax:      301-496-0887
> e-mail: fernando@mail.nih.gov
> www: http://usuarios.lycos.es/h2ax/
>
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