[Bioperl-l] module to find out primer binding sites in a genome sequence

[Torsten Seemann]

Gowthaman Ramasamy wrote:
> Hi List,
> Is there any module in bioperl which can find out the primer binding sites in a genomic sequence.
> I am interested in finding locations with few mismatches along the primer...not just the exact match (which is a very trivial task)

This FAQ question may help:
http://www.bioperl.org/wiki/FAQ#How_do_I_do_motif_searches_with_BioPerl.3F_Can_I_do_.22find_all_sequences_that_are_75.25_identical.22_to_a_given_motif.3F

This software may help:
http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi

-- 
Dr Torsten Seemann               http://www.vicbioinformatics.com
Victorian Bioinformatics Consortium, Monash University, Australia