Public Domain Software to change Restriction site on a Nucleic Acid Seq BY SILENT MUTATIONS

Basavaraju Shankarappa bsh at MED.PITT.EDU
Mon May 17 19:00:57 EST 1993

Dear Harry:
I would like to expand on some the information you provided.  
As to my knowledge, there are three programs available for the 
purpose of finding regions in a coding frame where restriction
enzyme recognition sites can be introduced by SILENT mutations.

The OligoMutantMaker is one for PC
The Silmut was our contribution for PC (BioTechniques 12:882
	Both of these are available from
For Macs, Weiner and Scheraga have written a similar program called
Gene.Design (CABIOS 5:191) [I don't know where this is available].

As to the Map program of GCG, I would never recommend this to anyone
trying to introduce RE sites by silent mutations.  The main reason
for this is that the /SIL flag can only identify those sites that can be
changed by silent mutations, provided they happen to be in the same 
reading frame as the input sequence.  I consider this to be a serious
handicap because there are several log-fold (?) differences in the number
of sites that can be identified by translating in three reading frames
as opposed to translating in one reading frame.  For example, for the 
restriction enzyme NdeI (CATATG), Map program will tell you that you 
can introduce this site only if you find His-Met (CACATG).  Whereas if you
translate this 6-base in three reading frames you will see that there are
65 additional tri-peptides where this site can be introduced by 
silent mutations.  These could be any combination of [SPTA-Y-VADEG]
and [FSYCLPHRITNVADG-I-CXW].  I hope GCG people will read this and try
to incorporate the features of above programs in their next version.
It was to our surprise and I am sure to those who identified this 
before us, that by simply translating the restriction enzyme recogn 
sequence in all three reading frames you get an ENORMOUS number of 
peptide motifs that are not easily obvious unless you think about it.  
Each of these peptide motif indicates the possibility of introducing 
the recogn sequence by silent mutations. 
Raj Shankarappa 
bsh at 
> >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 
> >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
> 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

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