Primer design with GCG

Tim Bolling bollingt at ugene1.abbott.com
Tue Jan 18 14:02:21 EST 1994

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.

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