Restriction assembly

RYBICKI, ED ED at micro.uct.ac.za
Thu Mar 24 03:27:07 EST 1994

> A fellow scientist asked me if there was a program (GCG or other)
> to generate a restriction map from actual restriction digest
> information without knowing any sequence information.  I looked
> through the GCG manual and could find nothing.  Does anyone
> know of a program to do this?  Thanks in advance for any
> help or advise.
There's a lot of things GCG is no good for...!  It's as clunky as a 
car designed by a committee of bicycle riders in the Stalinist central 
planning era - and if I could get a decent menu interface to WORK I 
would be a happy settler...!

As for restriction mapping, there is an extremely useful interactive 
mapping pgm called COMAP which we have taken to here in a big way: can 
take data read off gel, or even TIFF scanned image of gel in b and w 
(2 colour), and produce map.  Info appended for two systems:

This is the README file of COMAP V1.0a
COMAP is a public domain program for helping with the construction of
restriction maps of small DNA fragment from digestion data.
The program works under a graphical user interface, similar to the one 
with the protein analysis program PROFILEGRAPH.

COMAP does actually not calculate a map out of the digestion data but 
merely as a tool to help the user doing the work. for this purpose, 
the screen
is divided into a display for the map under construction and a display 
the 'gel' with the observed band pattern and, for comparison, the 
bands that
would result from the current map.
The user can insert, delete or move cuts in the map and simultaneously 
the resulting changes in the gel display.

If everything works ok, COMAP will be available from the major FTP 
for molecular biology programs and from the EMBL fileserver.

E-mail: send a mail to netserv at embl-heidelberg.de including the line

FTP:  as COMAP.ZIP from the following sites:

Help can be obtained from the author:
Kay Hofmann                                      Tel: +49 221 478-6980
Institut fuer Biochemie (med. Fak.)              Fax: +49 221 478-6979
Universitaet Koeln
Joseph Stelzmann Str. 52
D-5000 Koeln 41                INTERNET: 
khofmann at biomed.biolan.uni-koeln.de

And further: Eric Harley of our Dept Chem Path has written a DOS pgm 
which can map in a rather sophisticated way for you - given digest 
info - and also acts as a restriction map database, and can compare 
maps for phylogenetic/cluster analysis.  It costs some US$$$ (minimal) 
and can be got via: harley at chempath.uct.ac.za.

 | Ed Rybicki, PhD             |      "You got to...accen-tu-ate      |
 | (ed at micro.uct.ac.za)        |             The positive             |
 | Dept Microbiology           |       Ee-liminate the negative       |
 | University of Cape Town     |      Latch on to the affirmative     |
 |                             |   Don't mess with Mr In-be-tween..." |                      |
 | Private Bag, Rondebosch     |                                      |
 | 7700, South Africa          |              - Unknown               |
 | fax: xx27-21-650 4023       |           (Homefront, 1992)          |

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