Automation of DNA computing readout method implemented on lightcycler system
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...
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Institute of Electrical and Electronics Engineers
2009
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my.utm.132102011-07-21T06:08:40Z http://eprints.utm.my/id/eprint/13210/ Automation of DNA computing readout method implemented on lightcycler system Saaid, Muhammad Faiz Mohamed Ibrahim, Zuwairie Khalid, Marzuki Sarmin, Nor Haniza QA Mathematics TK Electrical engineering. Electronics Nuclear engineering 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. Institute of Electrical and Electronics Engineers 2009 Book Section PeerReviewed 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 http://dx.doi.org/10.1109/AMS.2009.80 doi:10.1109/AMS.2009.80 |
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QA Mathematics TK Electrical engineering. Electronics Nuclear engineering Saaid, Muhammad Faiz Mohamed Ibrahim, Zuwairie Khalid, Marzuki Sarmin, Nor Haniza Automation of DNA computing readout method implemented on lightcycler system |
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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.
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| format |
Book Section |
| author |
Saaid, Muhammad Faiz Mohamed Ibrahim, Zuwairie Khalid, Marzuki Sarmin, Nor Haniza |
| author_facet |
Saaid, Muhammad Faiz Mohamed Ibrahim, Zuwairie Khalid, Marzuki Sarmin, Nor Haniza |
| author_sort |
Saaid, Muhammad Faiz Mohamed |
| title |
Automation of DNA computing readout method implemented on lightcycler system |
| title_short |
Automation of DNA computing readout method implemented on lightcycler system |
| title_full |
Automation of DNA computing readout method implemented on lightcycler system |
| title_fullStr |
Automation of DNA computing readout method implemented on lightcycler system |
| title_full_unstemmed |
Automation of DNA computing readout method implemented on lightcycler system |
| title_sort |
automation of dna computing readout method implemented on lightcycler system |
| publisher |
Institute of Electrical and Electronics Engineers |
| publishDate |
2009 |
| url |
http://eprints.utm.my/id/eprint/13210/ http://dx.doi.org/10.1109/AMS.2009.80 |
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13.211869 |