software for silent mutagenesis

Basavaraju Shankarappa bsh at MED.PITT.EDU
Tue Jan 5 17:20:49 EST 1993


> In article <1992Dec30.185104.9506 at alw.nih.gov> usdin at helix.nih.gov (Ted Usdin) writes:
> >Weiner and Scheraga (CABIOS, vol 5 pp191-198, 1989) described a Macintosh
> >program (Gene.Design.?) to assist in introducing restriction sites into DNA without changing the amino
> >acid sequence.  Does anyone know where I can get a copy of this, or a similar
> >program that runs on a Macintosh?
> 
> There is a similar program which runs on a PC called OligoMutantMaker.
> It is available by anonymous ftp from:
> Host fly.bio.indiana.edu
> 
>     Location: /molbio/ibmpc
>            FILE -rw-r--r--       8540  May 14 1991  oligo.doc
>            FILE -rw-r--r--     231882  May 14 1991  oligo.uue
> Dan Jacobson
> danj at welchgate.welch.jhu.edu

	I would like to add that we have also developed a PC compatible
program called SILMUT for identifying regions for the introduction of 
restriction enzyme sites by silent mutagenesis.  Although we have used
the same principle as detailed in the above two programs our approach 
was highly simplified.  This programs just tells you what restriction
enzyme/s can be introduced by silent mutagenesis in a specific sequence
of amino or nucleic acid.  This program is most useful for those who are
contemplating introduction of RE sites to generate casette vectors or
for swapping specific fragments of a gene in a construct.  
	The program is also available on fly.bio.indiana.edu in the 
directory molbio/ibmpc as two files: Silmut.xxx.  
	The work has been published in Biotechinques 12: 882-884 (1992).
The program sets include source codes for the program which has been internally
documented.  The programs work in PC and unix machines but if anyone can 
make it work on a Mac, we would welcome that.

Raj Shankarappa
bsh at med.pitt.edu 




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