In article <m2u3rax32j.fsf at presto.med.upenn.edu>, jes at presto.med.upenn.edu
><Pine.SGI.3.94.961029194307.352B-100000 at leonardo.ls.huji.ac.il>
>yoramg2 at LEONARDO.LS.HUJI.AC.IL (Yoram Gerchman) writes:
>> I'm looking for a program that can find silent restriction sites. I have
> Silmut, but it limited to 100 enzymes that are 6-cutters.
>>Is this something generally needed? I've seen two requests here in
>the last month.
>>I recently wrote a Perl script to do this. It's not fancy but we've
>found it useful. It works best on Unix or Linux but I've also run it
>under MacPerl and it shoul work on just about any Perl platform. I've
>attached a sample run at the end of this message to give you a feel
>for what it does.
>>I'm reluctant to make it public until it's had wider testing. If
>anyone is interested in testing it and giving me some feedback, email
>me and I'll send it.
> Joe Smith
> University of Pennsylvania jes at presto.med.upenn.edu> Department of Physiology
> Philadelphia, PA 19104
>If people have acces to GCG all their mapping programs support the -silent
(/silent) option which, provided you start the sequence in the right
traduction phase, introduces silent sites for this phase. I find it most
usefull when used in combination with mapselect from EGCG which allows one to
recrate an enzyme file with non cutter or excluded enzymes of (for VMS
people) a DCL procedure called NOCUT which does the same job.
Pascal_Bochet at brown.edu