Automation of A DNA computing readout method based on real-time PCR implemented on a lightcycler system

Muhammad Faiz Mohamed Saaid, Zuwairie Ibrahim, Zulkifli M D Yusof, Junzo Watada

    Research output: Contribution to journalArticle

    2 Citations (Scopus)

    Abstract

    A DNA computer readout approach based on real-time polymerase chain reaction (PCR) for the computation of Hamiltonian Path Problem (HPP) is the main interest in this research. Based on this methodology, real-time amplification of DNA template with TaqMan probes is performed with some modifications to realize the readout. The readout approach consists of two phases: Real-time amplification in vitro followed by information processing in silico to assess the results of real-time amplification. The in silico information processing enables the extraction of the Hamiltonian path but the Taq-Man "YES" and "NO" reactions produced by real-time PCR need to be identified manually beforehand. Manual identification or classification limits the capability of automated readout. Hence, in this study, the readout approach is further improved by incorporating Fuzzy C-means clustering algorithm in the in silico information processing phase. As a result, automatic classification of the TaqMan "YES" and "NO" reactions is possible as demonstrated by the experimental results. Finally, an automated readout method can be realized as supported by the advantages of real-time PCR and Fuzzy C-means clustering algorithm.

    Original languageEnglish
    Pages (from-to)4263-4272
    Number of pages10
    JournalInternational Journal of Innovative Computing, Information and Control
    Volume6
    Issue number10
    Publication statusPublished - 2010 Oct

    Fingerprint

    DNA Computing
    Polymerase Chain Reaction
    Polymerase chain reaction
    Automation
    Amplification
    Hamiltonians
    DNA
    Real-time
    Clustering algorithms
    Information Processing
    Hamiltonian path
    Fuzzy C-means Clustering
    Clustering Algorithm
    Template
    Probe
    Methodology
    Experimental Results

    Keywords

    • DNA computing
    • Lightcycler system
    • Readout method
    • Real-time PCR
    • Taqman probe

    ASJC Scopus subject areas

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

    Cite this

    Automation of A DNA computing readout method based on real-time PCR implemented on a lightcycler system. / Saaid, Muhammad Faiz Mohamed; Ibrahim, Zuwairie; Yusof, Zulkifli M D; Watada, Junzo.

    In: International Journal of Innovative Computing, Information and Control, Vol. 6, No. 10, 10.2010, p. 4263-4272.

    Research output: Contribution to journalArticle

    Saaid, Muhammad Faiz Mohamed ; Ibrahim, Zuwairie ; Yusof, Zulkifli M D ; Watada, Junzo. / Automation of A DNA computing readout method based on real-time PCR implemented on a lightcycler system. In: International Journal of Innovative Computing, Information and Control. 2010 ; Vol. 6, No. 10. pp. 4263-4272.
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