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

[Sendu Bala]

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)

There's no module dedicated to that task, but Bioperl may help you to
answer the question.

Probably the easiest/reliable/clear thing to do is to do a Blast with
appropriate settings for short sequence with few mismatches. You can
write a script to only consider hits for your forward primer that are a
'primable' distance from a hit to your reverse primer (and check their
orientations are correct as well).

Or use some e-pcr tool.