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DNA Sequencing by Hybridization via Genetic Search

Author

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  • Jacek Blazewicz

    (Institute of Computing Science, Poznań University of Technology, Piotrowo 2, 60-965 Poznań, Poland, and the Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland)

  • Ceyda Oguz

    (Department of Industrial Engineering, Koç University, Istanbul, Turkey)

  • Aleksandra Swiercz

    (Institute of Computing Science, Poznań University of Technology, Piotrowo 2, 60-965 Poznań, Poland, and the Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland)

  • Jan Weglarz

    (Institute of Computing Science, Poznań University of Technology, Piotrowo 2, 60-965 Poznań, Poland, and the Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland)

Abstract

An innovative approach to DNA sequencing by hybridization utilizes isothermic oligonucleotide libraries. In this paper, we demonstrate the utility of a genetic algorithm for the combinatorial portion of this new approach by incorporating characteristics of DNA sequencing by hybridization in addition to isothermic oligonucleotide libraries. Specialized crossover and mutation operators were developed for this purpose. After initial experiments for parameter adjustment, the performance of the genetic algorithm approach was evaluated with respect to previous methods in the literature. The results indicate that the proposed new approach is superior to previous approaches. The proposed new crossover operator that inherits some features of the structured weighted combinations might also be of value for some other combinatorial problems, including the traveling salesman problem.

Suggested Citation

  • Jacek Blazewicz & Ceyda Oguz & Aleksandra Swiercz & Jan Weglarz, 2006. "DNA Sequencing by Hybridization via Genetic Search," Operations Research, INFORMS, vol. 54(6), pages 1185-1192, December.
    • Handle: RePEc:inm:oropre:v:54:y:2006:i:6:p:1185-1192
    DOI: 10.1287/opre.1060.0324
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    References listed on IDEAS

    as
    1. Blazewicz, J. & Formanowicz, P. & Kasprzak, M. & Markiewicz, W. T. & Weglarz, J., 2000. "Tabu search for DNA sequencing with false negatives and false positives," European Journal of Operational Research, Elsevier, vol. 125(2), pages 257-265, September.
    2. Ali E. Abbas & Susan P. Holmes, 2004. "Bioinformatics and Management Science: Some Common Tools and Techniques," Operations Research, INFORMS, vol. 52(2), pages 165-190, April.
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    Cited by:

    1. Blazewicz, Jacek & Kasprzak, Marta & Kierzynka, Michal & Frohmberg, Wojciech & Swiercz, Aleksandra & Wojciechowski, Pawel & Zurkowski, Piotr, 2018. "Graph algorithms for DNA sequencing – origins, current models and the future," European Journal of Operational Research, Elsevier, vol. 264(3), pages 799-812.
    2. Blazewicz, Jacek & Burke, Edmund K. & Kasprzak, Marta & Kovalev, Alexandr & Kovalyov, Mikhail Y., 2011. "The simplified partial digest problem: Approximation and a graph-theoretic model," European Journal of Operational Research, Elsevier, vol. 208(2), pages 142-152, January.

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