IUBio

Restriction Mapping Software

Dr Tan Tin Wee bchtantw at nuscc.nus.sg
Tue Jun 2 04:19:28 EST 1992


Some time ago, Douglas Brutlag wrote Keith Elliston,
regarding restriction mapping programs. 
Are any of these programs available in the public domain?
Are any of the authors reading this posting - I would appreciate
the contact?

I am not referring to programs such as COMAP where the user
has to manipulate the map, or programs that generate a map from
a sequence; rather, I refer to the following programs which "take
restriction fragment lengths and generate a map".

Thanks for any help.

Tin Wee Tan.
Department of Biochemistry, National University of Singapore.
bchtantw at nuscc.nus.sg


Attached posting fished out by WAISing biosci.src as follows:

Keith,

	There are many programs widely available that will take
restriction fragment lengths and generate a map.  Many of them require
complete enzyme digests and then use branch and bound methods to prune
the combinatoric tree of possible fragment permutations.  Others can
use partial enzyme digest data as well and are more adapted to modern
methods.

	The references for this area are:

Durand, R., and Bregegere, F. (1984).  An efficient program to
construct restriction maps from experimental data with realistic error
levels.  Nucleic. Acids. Res. 12, 703-716.

Fitch, W. M., Smith, T. F., and Ralph, W. W. (1983).  Mapping the
order of DNA restriction fragments.  Gene 22, 19-29.

Krawczak, M. (1988).  Algorithms for the restriction-site mapping of
DNA molecules.  Proc. Natl. Acad. Sci. U. S. A. 85, 7298-7301.

Nolan, G.P., Maina, C.V. and Szalay, A.A.  (1984).  Plasmid Mapping
computer program.  Nucleic Acids Res. 12, 717-729.

Pearson, W.  (1982).  Automatic construction of restriction site maps.
Nucleic Acids Research 10, 217-228.

Stefik, M.  (1978).  Inferring DNA structures from segmentation data.
Artificial Intelligence 11, 85-114.

Tuffery, P., Dessen, P., Mugnier, C., and Hazout, S. (1988).
Restriction map construction using a 'complete sentences
compatibility' algorithm.  Comput. Appl. Biosci. 4, 103-110.

	These programs run on platforms as varied as an IBM PC, SUN,
VAX, DEC-10 and Apple II.  Personally I use the MAP program from
IntelliGenetics which allows one to use both complete and partial
mapping data and recursive application of the program to complex data
so you can construct maps from hundreds of fragments.  This program
uses branch and bound on permutations of single enzyme complete
digests and uses partial enzyme digest data to further constrain the
permutations allowed.

Doug Brutlag
-- 
    Tin-Wee TAN                        /  INTERNET: bchtantw at nuscc.nus.sg
    Dept of Biochemistry               /  BITNET:   BCHTANTW at NUSVM
    National University of Singapore   /  Tel:      (65)-772-3678
    Singapore 0511                     /  Fax:      (65)-779-1453




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