Solving large double digestion problems for DNA restriction mapping by using branch-and-bound integer linear programming

Authors:
Z. Wu;Y. Zhang
Affiliations:
Department of Mathematics, Iowa State University, Ames, Iowa 50011, USA.;Department of Computational and Applied Mathematics, Houston, Texas 77005, USA
Venue:
International Journal of Bioinformatics Research and Applications
Year:
2008

Citing 3
Cited 0

Mapping DNA by stochastic relaxation

Advances in Applied Mathematics
Integer and combinatorial optimization

Integer and combinatorial optimization
Multiple solutions of DNA restriction mapping problems

Advances in Applied Mathematics

Quantified Score

Hi-index	0.00

Visualization

Abstract

The double digestion problem for DNA restriction mapping has been proved to be NP-complete and intractable if the numbers of the DNA fragments become large. Several approaches to the problem have been tested and proved to be effective only for small problems. In this paper, we formulate the problem as a mixed-integer linear program (MIP) by following (Waterman, 1995) in a sightly different form. With this formulation and using state-of-the-art integer programming techniques, we can solve randomly generated problems whose search space sizes are many-magnitude larger than previously reported testing sizes.