[Bioperl-l] counting and searching patterns

Marc Logghe Marc.Logghe at DEVGEN.com
Wed Jan 4 07:21:21 EST 2006

Hi Pierre,
Never used it myself, but can you do something with
Bio::Tools::SeqPattern ? Have a look at the FAQ:

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

> -----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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