mac prgram for creating silent mutations

[Doug Eernisse]

In article <genecutl-3009951500270001 at kosh-161b-1.berkeley.edu>,
genecutl at mendel.berkeley.edu (gc) wrote:

> <Hi to all:
> <        I am looking for a mac program like the silmut program for the PC
> <which helps one design silent mutations in genes to introduce restriction
> <sites. If anyone knows of such a program, please email information about
> <the program and how to get it. Thanks!
> 
> You can do it indirectly using MacVector.  Take your nucleotide 
> sequence and translate it into the amino acid sequence.  Then use 
> the reverse translate option on that to get back a degenerate
> nucleotide sequence.  Then you can search that for restriction sites
> to see all the possible sites that can be introduced into the
> DNA silently.

This is a neat idea. I like to think about programming such stuff.
I can easily get to the step where I have the degenerate nucleotide
sequence, but what is the easiest way to search a restriction site
database? Is there a list of all restriction enzymes that is publicly
available? Ideally, I would guess that one recognition sequence
per line, and nothing else, would be best, with the corresponding
names in a second file in the same order. Then one could march through
the sequence, say, 5 bases at a time, and try all possible combinations
anytime there is an ambiguous character. Any search hit gets saved along
with the current position. Sounds easy, but possibly slow, if such
a listing exists.

Email me if you have such a list -- my contributions would be freeware.

And I assume that there are site-directed mutagenesis methods available
so that one can actually do this? (Sorry for my naivete'.)

-- 
Doug Eernisse <DEernisse at fullerton.edu>
Dept. Biological Science MH282
California State University
Fullerton, CA 92634