Public Domain Software to change Restriction site

[bosborne at NATURE.BERKELEY.EDU]

	From BIOSCI-REQUEST at net.bio.net Mon May 17 10:33:55 1993
	Return-Path: <BIOSCI-REQUEST at net.bio.net>
	Received: from net.bio.net by insect.Berkeley.EDU (4.1/SMI-4.1.1)
		id AA00525; Mon, 17 May 93 10:33:44 PDT
	Received: by net.bio.net (5.65/IG-2.0) 
		id AA13998; Mon, 17 May 93 10:19:57 -0700
	Received: from sds.sdsc.edu by net.bio.net (5.65/IG-2.0) with SMTP 
		id AA13988; Mon, 17 May 93 10:19:48 -0700
	Received: from molly.sdsc.edu by Sdsc.Edu (sds.sdsc.edu STMG) via INTERNET;
	          Mon, 17 May 93 17:18:11 GMT
	Received: from [192.31.153.17] by molly.sdsc.edu (4.1/SMI-4.1)
		id AA20088; Mon, 17 May 93 10:18:21 PDT
	Message-Id: <9305171718.AA20088 at molly.sdsc.edu>
	Date: Mon, 17 May 1993 10:20:50 -0800
	To: root at mendel.berkeley.edu, computational-biology at net.bio.net,
	        bio-soft at net.bio.net
	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
   ------------------------------------------------------------