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...
| Main Authors: | , |
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| Format: | Book Section |
| Language: | English |
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Institute of Electrical and Electronics Engineering (IEEE)
2007
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| Online Access: | http://eprints.utm.my/9472/1/MuhammadFaiz2007InSilicoInformationProcessing.pdf |
| _version_ | 1796854520240668672 |
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| author | Mohamed Saaid, Muhammad Faiz Ibrahim, Zuwairie |
| author_facet | Mohamed Saaid, Muhammad Faiz Ibrahim, Zuwairie |
| author_sort | Mohamed Saaid, Muhammad Faiz |
| collection | ePrints |
| 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. |
| first_indexed | 2024-03-05T18:15:17Z |
| format | Book Section |
| id | utm.eprints-9472 |
| institution | Universiti Teknologi Malaysia - ePrints |
| language | English |
| last_indexed | 2024-03-05T18:15:17Z |
| publishDate | 2007 |
| publisher | Institute of Electrical and Electronics Engineering (IEEE) |
| record_format | dspace |
| spelling | utm.eprints-94722017-09-03T09:29:13Z http://eprints.utm.my/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/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 |
| 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 |
| title | 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_short | 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 |
| topic | QA75 Electronic computers. Computer science |
| url | http://eprints.utm.my/9472/1/MuhammadFaiz2007InSilicoInformationProcessing.pdf |
| work_keys_str_mv | AT mohamedsaaidmuhammadfaiz insilicoinformationprocessingfordnacomputingreadoutmethodbasedondnaengineopticon2system AT ibrahimzuwairie insilicoinformationprocessingfordnacomputingreadoutmethodbasedondnaengineopticon2system |