[Bioperl-l] counting and searching patterns

khoueiry khoueiry at ibdm.univ-mrs.fr
Wed Jan 4 04:42:16 EST 2006


    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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