Solving large double digestion problems for DNA restriction mapping by using branch-and-bound integer linear programming
by Z. Wu, Y. Zhang
International Journal of Bioinformatics Research and Applications (IJBRA), Vol. 4, No. 4, 2008

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.

Online publication date: Sat, 08-Nov-2008

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