Public Domain Software to change Restriction site

bosborne at NATURE.BERKELEY.EDU bosborne at NATURE.BERKELEY.EDU
Mon May 17 13:25:15 EST 1993


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	From: mangalam at salk-sc2.sdsc.edu (Harry Mangalam)
	X-Sender: mangalam at 192.31.153.12
	Subject: Re: Public Domain Software to change Restriction site on a Nucleic Acid Seq
	Status: RO

	>-- 
	>Hi, 1 of our Researchers would like to transform a nucleic acid sequence so
	>it keeps producing the same protein, but it could be cut with a restriction
	>enzyme. Is there some public domain software that can do that?

	   No, you have to do the work yourself.
	But seriously, there are a few options:  There's a freeware PC program
	called OligoMutantMaker which will do just that (available from the
	ftp.bio.indiana.edu archives), although I've never used it.
	   While it's not free, the widely available GCG Map program will search
	for sites that can be introduced by mutagenesis that will not change the
	translation by using the /SILent flag.
	   Probably others, as well, but that's all I can drag from slimy depths of
	my  memory at the moment.
	Cheers
	Harry



There is a program called silmut (for PC's and Suns and others)
that's available from ftp.bio.indiana.edu that does just that.
The C code would not compile and run on my NeXT so I had to tinker
with it. I also made it use a larger number of restriction enzymes
and expanded its database to contain all the 6-cutters found in
R. Robert's REBASE (from ncbi.nlm.nih.gov). If would like this 
modified code (compiles on NeXT and SGI) contact me. I apologize
for not finding the reference immediately, I will post it later.


   ------------------------------------------------------------
    Brian Osborne		  Plant Gene Expression Center
    bosborne at insect.berkeley.edu  Albany CA USA
   ------------------------------------------------------------




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