From: danj@welchgate.welch.jhu.edu (Dan Jacobson)
Subject: Re: software for silent mutagenesis
Organization: Johns Hopkins Univ. Welch Medical Library
Date: Wed, 30 Dec 1992 21:51:16 GMT

In article <1992Dec30.185104.9506@alw.nih.gov> usdin@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?
>
>Thanks for any help.
>

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


I am including some information about the program below.


Happy New Year,


Dan Jacobson

danj@welchgate.welch.jhu.edu


==============================================================================


OligoMutantMaker  (version 1.0)
Copyright 1987  Kevin Beadles, David Canter, Arnold Berk
("readme.doc" added 8/26/88, 2/24/89 by Spencer Yeh)


INTRODUCTION

   OligoMutantMaker simplifies the designing and screening of
oligonucleotide-directed single amino acid substitution experiments by
searching for nucleotide sequences which introduce a restriction
endonuclease recognition sequence into the codon substitution site of the
mutant.
   The program utilizes the redundancy of the genetic code to generate all
possible nucleotide sequences for a given amino acid substitution
(including nucleotide sequences in which silent mutations are introduced
into the 5' and/or 3' codons immediately adjacent to the substitution site)
and determines whether any restriction endonuclease recognition
sequences are present.  Any nucleotide sequence containing a restriction
site is displayed/printed along with relevant information about the site
such as its restriction enzyme(s), the random frequency of the enzyme's
recognition sequence(s), the prototype of the enzyme, isoschizomers of the
enzyme, and the unit cost of the enzyme from various biochemical
suppliers.


CONTACT ADDRESS

For questions about the program or suggestions for future improvements
please contact:

     Kevin Beadles
     1044 1/2 Shrader St.
     San Francisco, CA  94117
     
     tel.: (415) 759-0148   
     (Kevin will call you back collect if he must return your call.)



SYSTEMS SUPPORTED

An IBM compatible computer running MS-DOS is needed.


   



PROGRAM FILES before de-ARCing  

README.DOC      This documentation file.  
OLIGO.UUE	Archived and uuencoded file for both monochrome
                and color executable versions, and associated data
		files.  (234 Kb).



PROGRAM FILES after de-ARCing (Approx. 350 Kb total)

README.DOC       This documentation file
BWMUTANT.COM     Executable file for monochrome monitors
CMUTANT.COM      Executable file for color monitors
CUTTERS.DAT      Binary database of enzyme cleavage and availability data
CODONID.DAT      Standard genetic code
[ENZYME.TXT]     This file is created everytime the program is run.
                     It contains a copy of the results of the last analysis.


DOCUMENTATION


The program is internally documented with help messages.


(....)

ADDITIONAL INFORMATION ABOUT THE PROGRAM

Restriction Site Location:
   OligoMutantMaker searches for restriction sequences which have at
least one nucleotide in codon #0 (i.e. the codon to be substituted).  Since
the longest recognition sequence (GGCCNNNNNGGCC--Sfl I) spans thirteen
nucleotides, it is necessary to enter 27 nucleotides (twelve nucleotides on
either side of the three nucleotides which comprise codon #0) into the
program in order for it to function.

"Silent" Mutations:
   The program utilizes the redundancy of the genetic code to generate
all possible nucleotide sequences for the given amino acid substitution in
codon #0 (i.e. the codon to be substituted).  In addition to searching for
restriction sites which match these nucleotides sequences, the program
also examines those nucleotide sequences in which "silent" mutations have
been introduced into codon #-1 and codon #+1 (i.e. the codons immediately
upstream--or 5'--and downstream--or 3'--from codon #0, respectively)
and determines whether any additional restriction sites are created.  Only
those "silent" mutations which can be created by a single substitution in
the nucleotide closest to codon #0 (i.e. the third--or "wobble"--nucleotide
of codon #-1 and the first nucleotide of codon #+1) are examined.
Therefore, only five nucleotides (centered upon the middle nucleotide of
codon #0) are subject to substitution.


Abbreviations used in OligoMutantMaker:
   standard three letter amino acid abbreviations
      STP:  stop codon (UAA, UAG, or UGA)
   standard one letter nucleotide abbreviations
      N:  any nucleotide
      m:  methylated nucleotide
      /:  cleavage site
   standard restriction endonuclease abbreviations
   BMB:  Boehringer Mannheim Biochemicals
   BRL:  Bethesda Research Laboratories
   NEB:  New England Biolabs
   USBC:  United States Biochemical Corperation
   u:  unit(s)
   c/u:  cents/unit


Miscellaneous Notes:
   OligoMutantMaker recognizes 164 different restriction sites which are
      are cleaved by 126 different restriction enzymes.
   Price comparisons are based upon the smallest low concentration order
      available from each supplier.
   OligoMutantMaker does not search for cleavage specificities generated
      by methylating DNA with a selected restriction endonuclease (see NEB
      1986/87 Catalog p32 & p123 for further details).
   OligoMutantMaker does not note enzyme specificities resulting from
      star activity (NEB 1986/87 Catalog p86 & p121).



Bibliography:
Boehringer Mannheim Biochemicals, 1987/88 (Catalog)
Bethesda Research Laboratories, Catalog & Reference Guide (1985)
New England Biolabs, Catalog 1986/87
United States Biochemical Corporation, Enzymes & Reagents for
   Molecular Biology 1987