Does anybody know a good program to predict restriction sites, that
can be introduced into dna without changing protein sequence (silent
mutations). I have been using GMAP$ by Raghava (one of summer ussues
of Biotechniques, and pub/sortware/dos/ at EMBL server 188.8.131.52),
but it seems to have a very fat bug in the heart of the
search algorithm, that brings value of the predictions close to zero.
There are several algorithms published, but I could
not find any other working programs. If anybody knows anything about
this stuff, please let me know. Thanks for any information.