The GCG program PRIME does not allow what you want to do, that is, choose
a reverse primer and let the program search a forward primer. Either
PRIME searches both primers or (with parameter -primers=...) it tests
primer pairs you propose.
I know of a program that does what you want : PRIME from M.I.T.
(available ftp://genome.wi.mit.edu/distribution/primer.0.5). EGCG
contains a program TOPRIMER that translates a sequence in GCG format to
PRIME format. PRIME has however a strange feature : you can choose a
forward primer and the program will search for the reverse primer, but
if you try the opposite, that is, choose yourself the reverse primer,
PRIME takes the complement of your primer as forward primer. You can
however get get what you want by using the complement of your sequence.
Dr. Guy Bottu
