[Bioperl-l] counting and searching patterns
Marc.Logghe at DEVGEN.com
Wed Jan 4 07:21:21 EST 2006
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
> 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
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