Primer design from multiple alignment.

[Andrea Hansen]

Bill_A_Nussbaumer at ms.bd.com writes:


> I'm trying to find a computer program, preferably Win32 compatible but possibly
> Linux compatible that will identify optimal primer sequences for PCR based on a
> multiple sequence alignment.  i.e.  If I align a set of sequences from a single
> genus that have some variation, I would like to find the best primers to amplify
> all members of the set.  Any ideas would be most appreciated.

Hi Bill,
I think codehop is exactly the program you are looking for:

http://blocks.fhcrc.org/blocks/codehop.html
COnsensus-DEgenerate Hybrid Oligonucleotide Primers: PCR primers designed
from protein multiple sequence alignments.

Andrea
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