An ant colony system for solving DNA sequence design problem in DNA computing

Farhaana Yakop, Zuwairie Ibrahim, Amar Faiz Zainal Abidin, Zulkifli M. Yusof, Mohd Saberi Mohamad, Khairunizam Wan, Junzo Watada

    Research output: Contribution to journalArticle

    3 Citations (Scopus)

    Abstract

    Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic information used in the development and functioning of all known existing organisms. In DNA computing, a set of DNA sequences is involved in solving an optimisation problem. The design of those sequences is difficult because of the frequency of DNA sequence mismatch hybridisations. In this paper, an Ant Colony System approach for DNA sequence design is proposed to solve this DNA sequence design problem. A 4-node state transition machine was used in this study as the computation model. During the implementation, each ant was placed randomly at a start node and then moved according to the state transition rule. Once all of the ants completed the tour, the objective function was computed. This process was repeated until the maximum iteration was obtained. Seven ants were used to design seven sequences that were 20 nucleobases in length. The results showed that a set of usable DNA sequences can be produced using this method, which is better than previous approaches using the Genetic Algorithm and Multi-Objective Evolutionary Algorithm.

    Original languageEnglish
    Pages (from-to)7329-7339
    Number of pages11
    JournalInternational Journal of Innovative Computing, Information and Control
    Volume8
    Issue number10 B
    Publication statusPublished - 2012 Oct

    Keywords

    • Ant colony system
    • DNA computing
    • DNA sequence design

    ASJC Scopus subject areas

    • Computational Theory and Mathematics
    • Information Systems
    • Software
    • Theoretical Computer Science

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  • Cite this

    Yakop, F., Ibrahim, Z., Abidin, A. F. Z., Yusof, Z. M., Mohamad, M. S., Wan, K., & Watada, J. (2012). An ant colony system for solving DNA sequence design problem in DNA computing. International Journal of Innovative Computing, Information and Control, 8(10 B), 7329-7339.