Bruce Roe writes in reponse to M. Robersons inquiry into using GCG for testing
"specificity" of designed primers...
>Once you've got your primer designed, try:
>> FINDPATTERN /mismatch=3
>>That, on the VAX version of GCG will list all the matches in your target
>sequence, in your case HIV, with mismatches up to and including 3.
>With a 20+mer pcr primer, and a resonable annealing temperature, not
>much product should be seen from >3 mismatches.
While we are in agreement that this is about the best way you can utilize the
GCG package for this task, I would also add that this approach has many
shortcomings. Where priming is concerned - mismatching at the 3' end
(the end where extension takes place) has a far greater effect than mismatching
at the 5' end. I don't believe that any program which doesn't take that into
account will be able to predict specificity with very much accuracy.