Primer design from multiple alignment.

Olivier Friard friard at
Tue Jan 25 07:58:35 EST 2000

>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.


I wrote a DOS program to facilitate this kind of work. You must first
do a multi-alignment with CLUSTALW and then open the .ALN file with my
program. This program is called PRIMERS and it is free, try it at:



P.S. Actually I am working on the graphic version but the project is
not very avanced

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