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Automation of DNA computing readout method implemented on lightcycler system

Saaid, Muhammad Faiz Mohamed and Ibrahim, Zuwairie and Khalid, Marzuki and Sarmin, Nor Haniza (2009) Automation of DNA computing readout method implemented on lightcycler system. In: 2009 Third Asia International Conference on Modelling & Simulation. Article number 5071992 . Institute of Electrical and Electronics Engineers, New York, pp. 252-257. ISBN 978-076953648-4

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Official URL: http://dx.doi.org/10.1109/AMS.2009.80

Abstract

In this paper, an automation of DNA computing readout method based on real-time Polymerase Chan Reaction (PCR) is developed, which employs a hybrid in vitro-in silico approach. In the in vitro phase, TaqMan-based real-time PCR reactions are performed in parallel, to investigate the ordering of pairs of nodes in the Hamiltonian Path Problem (HPP), in terms of relative distance from the DNA sequence encoding the known start node. The real-time PCR experiment is implemented on LightCycler system. Fuzzy C-Means (FCM) clustering algorithm is used to identify automatically two different reactions in real-time PCR, followed by in silico algorithm, which in turn, enables extraction of the Hamiltonian path. A software called SILICOLIGHT is built to implement the FCM clustering and the in silico algorithm, which return the desired Hamiltonian path.

Item Type:Book Section
Additional Information:2009 3rd Asia International Conference on Modelling and Simulation, AMS 2009; Bandung, Bali; 25 May 2009 through 26 May 2009
Uncontrolled Keywords:DNA-computing, FCM clustering, Fuzzy c-means clustering algorithms, Hamiltonian path
Subjects:Q Science > QA Mathematics
T Technology > TK Electrical engineering. Electronics Nuclear engineering
Divisions:Electrical Engineering
ID Code:13210
Deposited By: Ms Zalinda Shuratman
Deposited On:21 Jul 2011 06:08
Last Modified:21 Jul 2011 06:08

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