counting and searching patterns

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counting and searching patterns

khoueiry

 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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RE: counting and searching patterns

Marc Logghe
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: [hidden email]
> [mailto:[hidden email]] On Behalf Of khoueiry
> Sent: Wednesday, January 04, 2006 10:42 AM
> To: [hidden email]
> 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
>
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

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RE: 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: [hidden email]
> > [mailto:[hidden email]] On Behalf Of khoueiry
> > Sent: Wednesday, January 04, 2006 10:42 AM
> > To: [hidden email]
> > 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
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > [hidden email]
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
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