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

[Sean Davis]

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)
>   

See here:

http://genome.ucsc.edu/cgi-bin/hgPcr?command=start

It is designed for exactly this task, is very fast, is available as an 
executable or web-based (though watch the usage requirements), and the 
output can be parsed rather easily.

Sean