Automation of DNA computing readout method based on real-time PCR implemented on DNA engine opticon 2 system

Muhammad Faiz Mohamed Saaid; Ismail Ibrahim; Shahdan Sudin; Mohd Saberi Mohamad; Zulkifli Md Yusof; Jameel Abdulla Ahmed Mukred; Kamal Khalil; Zuwairie Ibrahim; Junzo Watada

Automation of DNA computing readout method based on real-time PCR implemented on DNA engine opticon 2 system

Muhammad Faiz Mohamed Saaid, Ismail Ibrahim, Shahdan Sudin, Mohd Saberi Mohamad, Zulkifli Md Yusof, Jameel Abdulla Ahmed Mukred, Kamal Khalil, Zuwairie Ibrahim, Junzo Watada

Research output: Contribution to journal › Article › peer-review

1 Citation (Scopus)

Abstract

Previously, an automation of a DNA computing readout method for the Hamiltonian Path Problem (HPP) has been implemented based on LightCycler System. In this study, a similar readout approach is implemented based on DNA Engine Opticon 2 System. The readout approach consists of two steps: real-time amplification in vitro using TaqMan-based real-time PCR, followed by an in silico phase. The in silico phase consists of a data clustering algorithm and an information processing to extract the Hamiltonian path after the TaqMan \YES and \NO reactions have been identified. The result indicates that the automation of DNA computing readout method can be efficiently implemented on DNA Engine Opticon 2 System.

Original language	English
Pages (from-to)	1907-1916
Number of pages	10
Journal	International Journal of Innovative Computing, Information and Control
Volume	8
Issue number	3 A
Publication status	Published - Mar 2012
Externally published	Yes

Keywords

Dna computing
Hamiltonian path problem
Real-time PCR

ASJC Scopus subject areas

Software
Theoretical Computer Science
Information Systems
Computational Theory and Mathematics

Cite this

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title = "Automation of DNA computing readout method based on real-time PCR implemented on DNA engine opticon 2 system",

abstract = "Previously, an automation of a DNA computing readout method for the Hamiltonian Path Problem (HPP) has been implemented based on LightCycler System. In this study, a similar readout approach is implemented based on DNA Engine Opticon 2 System. The readout approach consists of two steps: real-time amplification in vitro using TaqMan-based real-time PCR, followed by an in silico phase. The in silico phase consists of a data clustering algorithm and an information processing to extract the Hamiltonian path after the TaqMan \YES and \NO reactions have been identified. The result indicates that the automation of DNA computing readout method can be efficiently implemented on DNA Engine Opticon 2 System.",

keywords = "Dna computing, Hamiltonian path problem, Real-time PCR",

author = "Saaid, {Muhammad Faiz Mohamed} and Ismail Ibrahim and Shahdan Sudin and Mohamad, {Mohd Saberi} and Yusof, {Zulkifli Md} and Mukred, {Jameel Abdulla Ahmed} and Kamal Khalil and Zuwairie Ibrahim and Junzo Watada",

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language = "English",

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T1 - Automation of DNA computing readout method based on real-time PCR implemented on DNA engine opticon 2 system

AU - Saaid, Muhammad Faiz Mohamed

AU - Ibrahim, Ismail

AU - Sudin, Shahdan

AU - Mohamad, Mohd Saberi

AU - Yusof, Zulkifli Md

AU - Mukred, Jameel Abdulla Ahmed

AU - Khalil, Kamal

AU - Ibrahim, Zuwairie

AU - Watada, Junzo

PY - 2012/3

Y1 - 2012/3

N2 - Previously, an automation of a DNA computing readout method for the Hamiltonian Path Problem (HPP) has been implemented based on LightCycler System. In this study, a similar readout approach is implemented based on DNA Engine Opticon 2 System. The readout approach consists of two steps: real-time amplification in vitro using TaqMan-based real-time PCR, followed by an in silico phase. The in silico phase consists of a data clustering algorithm and an information processing to extract the Hamiltonian path after the TaqMan \YES and \NO reactions have been identified. The result indicates that the automation of DNA computing readout method can be efficiently implemented on DNA Engine Opticon 2 System.

AB - Previously, an automation of a DNA computing readout method for the Hamiltonian Path Problem (HPP) has been implemented based on LightCycler System. In this study, a similar readout approach is implemented based on DNA Engine Opticon 2 System. The readout approach consists of two steps: real-time amplification in vitro using TaqMan-based real-time PCR, followed by an in silico phase. The in silico phase consists of a data clustering algorithm and an information processing to extract the Hamiltonian path after the TaqMan \YES and \NO reactions have been identified. The result indicates that the automation of DNA computing readout method can be efficiently implemented on DNA Engine Opticon 2 System.

KW - Dna computing

KW - Hamiltonian path problem

KW - Real-time PCR

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Automation of DNA computing readout method based on real-time PCR implemented on DNA engine opticon 2 system

Abstract

Keywords

ASJC Scopus subject areas

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