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Physical Mapping of Chromosomes: A Combinatorial Problem in Molecular Biology
 

Summary: Physical Mapping of Chromosomes: A Combinatorial Problem
in Molecular Biology
Farid Alizadeh \Lambda Richard M. Karp \Lambday Lee A. Newberg y
Deborah K. Weisser y
1 Introduction
A DNA molecule such as a chromosome is a very long polymer consisting of two intertwined
strands, each of which is a sequence of nucleotides from the set fA; T ; C;Gg. The nucleotides
A and T are complementary to each other, as are the nucleotides C and G. Each nucleotide
on one strand is bound to a complementary nucleotide on the other strand. The human
genome project and many other efforts in molecular biology aim to sequence the chromosomes
of humans and other species and to elucidate the genetic information contained in these
sequences.
In order to study a large DNA molecule it is necessary to break it into smaller pieces, study
the structure of each piece, and then mathematically reassemble the pieces to determine the
structure of the entire molecule. This paper is concerned with algorithms for the reassembly
process.
Restriction enzymes can be used to cut a long DNA molecule into fragments. Under
appropriate experimental conditions a given restriction enzyme will cleave a DNA molecule
at every site where a certain short sequence of nucleotides occurs. A separation process called
electrophoresis can be used to separate the resulting fragments of the DNA molecule and

  

Source: Alizadeh, Farid - Rutgers Center for Operations Research, Rutgers University

 

Collections: Mathematics