Abstract
In this work, particle swarm optimization (PSO) is applied to automate the DNA computing readout method based on a real-time polymerase chain reaction (PCR). Moreover, real-time amplification was performed and the TaqMan detection approach was used for the plan and the readout approach development. The most important part of the readout method is identifying two different reactions in the real-time PCR, which involve in vitro and in silico processes in order to inspect the placement of pairs of nodes in the Hamiltonian path problem. In addition, the real-time PCR experiment is implemented on the LightCycler System. Previously, manual method was exploited to classify two different output reactions of real-time PCR that was a time consuming process. In this study, by exploiting MATLAB the PSO has been implemented for clustering output reactions of real-time PCR and experimental results depict that the amplification response for “YES” and “NO” reactions can be clustered correctly.
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Mullis K., Faloona F., Scharf S., Saiki R., Horn G., Erlich H.: Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb. Symp. Quant. Biol. 51, 263–273 (1986)
Overbergh L., Giulietti A., Valckx D., Decallonne B., Bouillon R., Mathieu C.: The use of real-time reverse transcriptase PCR for the quantification of cytokine gene expression. J. Biomol. Tech. 14(1), 33–43 (2003)
Walker N.J.: A technique whose time has come. Science 296, 557–559 (2002)
Lakowicz J.R.: Principles of Fluorescence Spectroscopy vol. 3. Kluwer Academic/Plenum Publishers, New York (2006)
Ibrahim Z., Rose J.A., Tsuboi Y., Ono O., Khalid M.: A new readout approach in DNA computing based on real-time PCR with TaqMan probes. In: Mao, C., Yokomori, T. (eds.) Lecture Notes in Computer Science (LNCS), vol. 4287, pp. 350–359. Springer-Verlag, Berlin (2006)
Adleman L.M.: Molecular computation of solutions to combinatorial problems. Science 266, 1021–1024 (1994)
Rose, J.A.; Deaton, R.; Garzon, M.; Stevens, S.E. Jr.: The effect of uniform melting temperatures on the efficiency of DNA computing. In: DIMACS Workshop on DNA Based Computers III, pp. 35–42 (1997)
Wood D.H., Clelland C.L.T., Bancroft C.: Universal biochip readout of directed Hamiltonian path problems. Lect. Notes Comput. Sci. 2568, 168–181 (1999)
Saaid, M.F.M.; Ibrahim, Z.; Khalid, M.; Sarmin, N.H.; Rose, J.: Fuzzy C-means clustering for DNA computing readout method implemented on LightCycler system. In: Proceedings of SICE International Conference. Chofu, Japan, 20–23 August 2008, pp. 676–681 (2008)
Omran, M.; Salman, A.; Engelbrecht, A.P.: Image classification using particle swarm optimization. In: Conference on Simulated Evolution and Learning, vol. 1, pp. 370–374 (2002)
Kennedy, J.; Eberhart, R.C.: Particle swarm optimization. In: Proceedings of IEEE International Conference on Neural Networks, Perth, Australia, vol. 4, pp. 1942–1948 (1995)
Kennedy J., Eberhart R.C., Shi Y.: Swarm Intelligence. Morgan Kaufmann Academic Press, New York (2001)
Poli, R.: Analysis of the publications on the applications of particle swarm optimization. J. Artif. Evol. Appl. 2008:685175 (2008)
Abraham A., Das S., Roy S.: Swarm intelligence algorithms for data clustering. In: Maimon, O., Rokach, L. (eds.) Soft Computing for Knowledge Discovery and Data Mining, pp. 279–313. Springer Verlag, Germany (2007)
Ko C.N., Chang Y.P., Wu C.J.: An orthogonal-array-based particle swarm optimizer with nonlinear time-varying evolution. Appl. Math. Comput. 191, 272–279 (2007)
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Maghsoudi, M.J., Ibrahim, Z., Buyamin, S. et al. Data Clustering for the DNA Computing Readout Method Implemented on LightCycler and Based on Particle Swarm Optimization. Arab J Sci Eng 37, 697–707 (2012). https://doi.org/10.1007/s13369-012-0196-3
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DOI: https://doi.org/10.1007/s13369-012-0196-3