Silent mutation software

Pascal_Bochet Pascal_Bochet at brown.edu
Fri Nov 1 11:52:20 EST 1996


In article <m2u3rax32j.fsf at presto.med.upenn.edu>, jes at presto.med.upenn.edu 
says...
>
>
>In article
><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
>---
> 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





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