[Bioperl-l] Fuzzy matching sequences

[Kris Boulez]

[ It's well possible that there isn't a solution for my problem in
BioPerl, but as it's a biology problem I'm trying to solve with perl and
there are Perl experts on the list ... ]

I've been asked to check if a certain x-mer ( 15 < x < 20 ) is present
in some sequences. This works fine using a regex. Now the biologists
come and ask if there are sequences containing the x-mer when allowing
one point mutation (anywhere in the overlap). To make things even worse:
some of these sequences contain N .

Do people know of a way to do this using perl regexes (I couldn't find
anything in the Friedl book). The only solution I can think of is to
create a blastable DB from the x-mers and blast all sequences against
this DB. 

Any other ideas ?


Kris,