[Bioperl-l] counting and searching patterns

[khoueiry]

thanks Marc,

    I forgot to look to the great wiki page so it helps me to keep it in
mind. Actually, SeqPattern don't do the stuff neither the TFBS package
that works for matrices and I'm forced to use a consensus. The idea to
use fuzznuc from EMBOSS may be of importance for me and I'll see what i
can do with it. 

regards
Pierre




On Wed, 2006-01-04 at 13:21 +0100, Marc Logghe wrote:

> Hi Pierre,
> Never used it myself, but can you do something with
> Bio::Tools::SeqPattern ? Have a look at the FAQ:
> http://bioperl.open-bio.org/wiki/FAQ#How_do_I_do_motif_searches_with_Bio
> Perl.3F_Can_I_do_.22find_all_sequences_that_are_75.25_identical.22_to_a_
> given_motif.3F
> 
> You could also do it with EMBOSS' fuzznuc:
> On the command line you do: 
> fuzznuc <your_seq_file> -pattern MGGAAR -complement 
> If you need to automate this, you can launch fuzznuc with bioperl.
> To do that you will need Bio::Factory::EMBOSS which is part of
> bioperl-run.
> HTH
> Cheers,
> Marc
> 
> 
> 
> > -----Original Message-----
> > From: bioperl-l-bounces at portal.open-bio.org 
> > [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of khoueiry
> > Sent: Wednesday, January 04, 2006 10:42 AM
> > To: bioperl-l at bioperl.org
> > Subject: [Bioperl-l] counting and searching patterns
> > 
> > 
> >  Hello,
> > 
> >     It's been a while that I'm working on an issue and the 
> > matter of finding the best way to do it is triggering me. 
> > Actually, I want to count/search a pattern in a nucleotide 
> > sequence. (i.e : search/count for MGGAAR). What I'm doing now 
> > is to Generates unique Seq objects using :IUPAC:module, then 
> > for each unique seq generates the reverse one using  
> > :SeqPattern: and going to count/search in my seq.
> > 
> > 
> > i.e : MGGAAR -> C/AGGAAG/A (IUPAC) 4 possibilities + 4 
> > reverse ( :SeqPattern:) = 8 .
> > 
> > 
> > I was wondering, if there is a bioperl way to do the 
> > count/search directly using the initial pattern (MGGAAR) 
> > taking the reverse case into account (that is YTTCCK in my example).
> > 
> > 
> > Any help or suggestions are appreciated
> > 
> > 
> > Thanks to all and happy new year
> > 
> > pierre
> > 
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