In silico information processing for DNA computing readout method based on DNA engine opticon 2 system

In this paper, a novel readout approach for the Hamiltonian path problem (HPP) in DNA computing based on the real-time polymerase chain reaction (PCR) is proposed. Based on this approach, real-time amplification was performed with the TaqMan probes and the TaqMan detection mechanism was exploited fo...

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Main Authors: Mohamed Saaid, Muhammad Faiz, Ibrahim, Zuwairie
Format: Book Section
Language:English
Published: Institute of Electrical and Electronics Engineering (IEEE) 2007
Subjects:
Online Access:http://eprints.utm.my/id/eprint/9472/1/MuhammadFaiz2007InSilicoInformationProcessing.pdf
http://eprints.utm.my/id/eprint/9472/
http://dx.doi.org/10.1109/SCORED.2007.4451406
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spelling my.utm.94722017-09-03T09:29:13Z http://eprints.utm.my/id/eprint/9472/ In silico information processing for DNA computing readout method based on DNA engine opticon 2 system Mohamed Saaid, Muhammad Faiz Ibrahim, Zuwairie QA75 Electronic computers. Computer science In this paper, a novel readout approach for the Hamiltonian path problem (HPP) in DNA computing based on the real-time polymerase chain reaction (PCR) is proposed. Based on this approach, real-time amplification was performed with the TaqMan probes and the TaqMan detection mechanism was exploited for the design and development of the proposed readout approach. The readout approach consists of two phases: real-time amplification in vitro using TaqMan- based real-time PCR, followed by information processing in silico to assess the results of real-time amplification, which in turn, enables the extraction of the Hamiltonian path. In this paper, instead of using manual clustering of two different reactions in real-time PCR, a computer system is developed such that the clustering can be done automatically. This clustering process can be done quickly based on the number of nodes in the HPP problems and the TaqMan reactions and the data obtained previously is used to extract the correct Hamiltonian path. Institute of Electrical and Electronics Engineering (IEEE) 2007-12 Book Section PeerReviewed application/pdf en http://eprints.utm.my/id/eprint/9472/1/MuhammadFaiz2007InSilicoInformationProcessing.pdf Mohamed Saaid, Muhammad Faiz and Ibrahim, Zuwairie (2007) In silico information processing for DNA computing readout method based on DNA engine opticon 2 system. In: The 5th Student Conference on Research and Development –SCOReD 2007. Institute of Electrical and Electronics Engineering (IEEE), pp. 1-6. ISBN 978-1-4244-1469-7 http://dx.doi.org/10.1109/SCORED.2007.4451406 doi : 10.1109/SCORED.2007.4451406
institution Universiti Teknologi Malaysia
building UTM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Teknologi Malaysia
content_source UTM Institutional Repository
url_provider http://eprints.utm.my/
language English
topic QA75 Electronic computers. Computer science
spellingShingle QA75 Electronic computers. Computer science
Mohamed Saaid, Muhammad Faiz
Ibrahim, Zuwairie
In silico information processing for DNA computing readout method based on DNA engine opticon 2 system
description In this paper, a novel readout approach for the Hamiltonian path problem (HPP) in DNA computing based on the real-time polymerase chain reaction (PCR) is proposed. Based on this approach, real-time amplification was performed with the TaqMan probes and the TaqMan detection mechanism was exploited for the design and development of the proposed readout approach. The readout approach consists of two phases: real-time amplification in vitro using TaqMan- based real-time PCR, followed by information processing in silico to assess the results of real-time amplification, which in turn, enables the extraction of the Hamiltonian path. In this paper, instead of using manual clustering of two different reactions in real-time PCR, a computer system is developed such that the clustering can be done automatically. This clustering process can be done quickly based on the number of nodes in the HPP problems and the TaqMan reactions and the data obtained previously is used to extract the correct Hamiltonian path.
format Book Section
author Mohamed Saaid, Muhammad Faiz
Ibrahim, Zuwairie
author_facet Mohamed Saaid, Muhammad Faiz
Ibrahim, Zuwairie
author_sort Mohamed Saaid, Muhammad Faiz
title In silico information processing for DNA computing readout method based on DNA engine opticon 2 system
title_short In silico information processing for DNA computing readout method based on DNA engine opticon 2 system
title_full In silico information processing for DNA computing readout method based on DNA engine opticon 2 system
title_fullStr In silico information processing for DNA computing readout method based on DNA engine opticon 2 system
title_full_unstemmed In silico information processing for DNA computing readout method based on DNA engine opticon 2 system
title_sort in silico information processing for dna computing readout method based on dna engine opticon 2 system
publisher Institute of Electrical and Electronics Engineering (IEEE)
publishDate 2007
url http://eprints.utm.my/id/eprint/9472/1/MuhammadFaiz2007InSilicoInformationProcessing.pdf
http://eprints.utm.my/id/eprint/9472/
http://dx.doi.org/10.1109/SCORED.2007.4451406
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score 13.222552