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DNA Sequencing—Tabu and Scatter Search Combined

Jacek Baewicz, Fred Glover, Marta Kasprzak

Institute of Computing Science, Pozna University of Technology, Piotrowo 3A, 60-965 Pozna, Poland, and Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12, 61-704 Pozna, Poland
Leeds School of Business, University of Colorado, Boulder, Colorado 80309-0419, USA
Institute of Computing Science, Pozna University of Technology, Piotrowo 3A, 60-965 Pozna, Poland, and Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12, 61-704 Pozna, Poland
blazewic{at}put.poznan.pl
fred.glover{at}colorado.edu
marta{at}cs.put.poznan.pl

In this paper, a tabu-search algorithm enhanced by scatter search is presented. The algorithm solves the DNA sequencing problem with negative and positive errors, yielding outcomes of high quality. We compare the new method with two other metaheuristic approaches: a previous tabu-search method and a hybrid genetic algorithm, and also with an old branch-and-bound approach.

Key words: heuristics; integer programming; computational molecular biology
History: received April 2001; revised May 2003; accepted July 2003.

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				J. Blazewicz, C. Oguz, A. Swiercz, and J. Weglarz DNA Sequencing by Hybridization via Genetic Search Operations Research, November 1, 2006; 54(6): 1185 - 1192. [Abstract] [PDF]