* MSDOS Restriction site programs

Dan Jacobson danj at WELCHGATE.WELCH.JHU.EDU
Fri Mar 27 18:10:35 EST 1992


Steve Kilpatrick writes:

>I'm looking for a program for MS-DOS that can identify restriction sites
>from sequence data for a number of enzymes. Ideally, I'd like to find one
>that can also identify sequences that are one step away from restriction
>sites, and that is available via anonymous ftp.


Well two programs jump to mind that will do what you`re looking for, Oligo
and Marker.  Both run under MSDOS and are different from one another - 
I'm including the docs so that you can get and idea what they do, as well
as the ftp site where you can get them.  Kudos go to the authors and the 
ftp site managers.


Hope this Helps,

Dan Jacobson

danj at 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.



STARTING THE PROGRAM

The ".uue" files in the downloadable version require both the
UUDECODE program and an "ARC"-compatible dearchiving program such as
PKUNPAK or ARCE to restore the executable file. 


".UUE" files:

First decode the ".uue" file:

	>UUDECODE oligo.uue

Then dearchive the resulting ".arc" file to an appropriate directory by
using PKUNPAK (or compatible program):

	>PKUNPAK oligo.arc c:\oligo


Once installed, CD to the appropriate directory and then start the
program by typing its name at the MS-DOS prompt:

     >BWMUTANT         (for monochrome monitors)

or   >CMUTANT          (for color monitors)

It is recommended that the user copy the program files to hard disk so
that more disk space will be available to the program.


SAMPLE PROGRAM OUTPUT

The following is abreviated output from a sample run to give an idea of
how the program works:

   OligoMutantMaker requires the entry of nine codons (27 nucleotides)
from the "sense"--or mRNA-homologous--strand of DNA.  The codons are
are numbered "-4" through "+4" (upstream-to-downstream or 5'-to-3')
where codon #0 is the codon to be substituted.  The codons must be entered
individually using standard one letter nucleotide abbreviations (A, C, G, T
or U) as they are requested.

(The user enters the 27 nucleotide fragment at this point)

Nucleotide #         1   4   7   10  13  16  19  22  25

Nucleotide Sqn       GGG GGG GGG GGG GGG GGG GGG GGG GGG

Codon #              -4  -3  -2  -1   0   1   2   3   4

Amino Acid Sqn       GLY GLY GLY GLY GLY GLY GLY GLY GLY

(Once the fragment is entered, the user picks an amino acid replacement
for the central codon)

 1) ALA   2) ARG   3) ASN   4) ASP   5) CYS   6) GLN   7) GLU   8) GLY
 9) HIS  10) ILE  11) LEU  12) LYS  13) MET  14) PHE  15) PRO  16) SER
17) THR  18) TRP  19) TYR  20) VAL  21) STP

Please enter the number of the amino acid that you want to insert
at codon #0: 14

   <D>isplay  <P>rint  <R>estart

(The results are then displayed.  Lowercase letters indicate altered
base pairs.  In the description of the recognition sequence, the "/"'s
indicate where the enzyme cuts on each of the strands.)

GGG GGG GGG GGa ttc GGG GGG GGG GGG -- the recognition sequence is GANTC
             -- ---
Hinf I   5' G/ANT C
         3' C TNA/G
         random site frequency:  1/256
         isoschizomers:  FnuA I, Hha II, Nca I, Nov II, NsiH I, Hine I
         BMB:  4.4c/u  1000u  $44
         BRL:  4c/u  1000u  $40
         NEB:  1.1c/u  5000u  $55
         USBC:  3.5c/u  1000u  $35


   <D>isplay  <P>rint  <R>estart


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



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

Host genbank.bio.net

    Location: /pub/dos
           FILE -rw-rw-r--       8099  Oct 26 1989  oligo.doc
           FILE -rw-rw-r--     231882  Feb 25 1989  oligo.uue


------------------------------------------------------------------------

DOS only

MARKER V1.0 - DOCUMENTATION


Copyright 1991 by Stefan Rensing.




General description :

MARKER



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