A DNA sequence design for molecular computation of hamiltonian path problem with output visualization based on real-time PCR
It is already been proven that it is possible to solve mathematical graph problem such as the Hamiltonian Path Problem (HPP), Traveling Salesman Problem (TSP), and the Shortest Path Problem (SPP), by means of molecular computing. Normally, in molecular computation, the DNA sequences used for the com...
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| Format: | Article |
| Language: | English |
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Faculty of Electrical Engineering
2008
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| Online Access: | http://eprints.utm.my/9927/ http://eprints.utm.my/9927/1/ZuwairieIbrahim2008_ADNASequenceDesignForMplecularComputation.pdf |
| _version_ | 1848891976884158464 |
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| author | Ibrahim, Zuwairie Kurniawan, Tri Basuki Sarmin, Nor Haniza Khalid, Marzuki |
| author_facet | Ibrahim, Zuwairie Kurniawan, Tri Basuki Sarmin, Nor Haniza Khalid, Marzuki |
| author_sort | Ibrahim, Zuwairie |
| building | UTeM Institutional Repository |
| collection | Online Access |
| description | It is already been proven that it is possible to solve mathematical graph problem such as the Hamiltonian Path Problem (HPP), Traveling Salesman Problem (TSP), and the Shortest Path Problem (SPP), by means of molecular computing. Normally, in molecular computation, the DNA sequences used for the computation should be critically designed in order to reduce error that could occur during computation. In the previous paper, we have proposed a new readout method tailored specifically to HPP in DNA computing using real-time PCR for output visualization. Six nodes HPP was considered. Based on the example instance, the method requires 11 oligonucleotides, where 6 oligonucleotides are for the nodes and 5 oligonucleotides are for the edges. Three TaqMan probes and five primers are required as well. In this study, a procedure for DNA sequence design is presented in order to obtain good sequences for those nodes, primers, and probes. The experiment is done based on the generated DNA sequences and the Hamiltonian Path can be determined successfully |
| first_indexed | 2025-11-15T21:06:32Z |
| format | Article |
| id | utm-9927 |
| institution | Universiti Teknologi Malaysia |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T21:06:32Z |
| publishDate | 2008 |
| publisher | Faculty of Electrical Engineering |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | utm-99272010-06-22T08:21:14Z http://eprints.utm.my/9927/ A DNA sequence design for molecular computation of hamiltonian path problem with output visualization based on real-time PCR Ibrahim, Zuwairie Kurniawan, Tri Basuki Sarmin, Nor Haniza Khalid, Marzuki TK Electrical engineering. Electronics Nuclear engineering It is already been proven that it is possible to solve mathematical graph problem such as the Hamiltonian Path Problem (HPP), Traveling Salesman Problem (TSP), and the Shortest Path Problem (SPP), by means of molecular computing. Normally, in molecular computation, the DNA sequences used for the computation should be critically designed in order to reduce error that could occur during computation. In the previous paper, we have proposed a new readout method tailored specifically to HPP in DNA computing using real-time PCR for output visualization. Six nodes HPP was considered. Based on the example instance, the method requires 11 oligonucleotides, where 6 oligonucleotides are for the nodes and 5 oligonucleotides are for the edges. Three TaqMan probes and five primers are required as well. In this study, a procedure for DNA sequence design is presented in order to obtain good sequences for those nodes, primers, and probes. The experiment is done based on the generated DNA sequences and the Hamiltonian Path can be determined successfully Faculty of Electrical Engineering 2008-12 Article PeerReviewed application/pdf en http://eprints.utm.my/9927/1/ZuwairieIbrahim2008_ADNASequenceDesignForMplecularComputation.pdf Ibrahim, Zuwairie and Kurniawan, Tri Basuki and Sarmin, Nor Haniza and Khalid, Marzuki (2008) A DNA sequence design for molecular computation of hamiltonian path problem with output visualization based on real-time PCR. Elektrika, 10 (2). pp. 59-64. ISSN 0128-4428 http://www.fke.utm.my/elektrika/dec08/paper10dec08.pdf |
| spellingShingle | TK Electrical engineering. Electronics Nuclear engineering Ibrahim, Zuwairie Kurniawan, Tri Basuki Sarmin, Nor Haniza Khalid, Marzuki A DNA sequence design for molecular computation of hamiltonian path problem with output visualization based on real-time PCR |
| title | A DNA sequence design for molecular computation of hamiltonian path problem with output visualization based on real-time PCR |
| title_full | A DNA sequence design for molecular computation of hamiltonian path problem with output visualization based on real-time PCR |
| title_fullStr | A DNA sequence design for molecular computation of hamiltonian path problem with output visualization based on real-time PCR |
| title_full_unstemmed | A DNA sequence design for molecular computation of hamiltonian path problem with output visualization based on real-time PCR |
| title_short | A DNA sequence design for molecular computation of hamiltonian path problem with output visualization based on real-time PCR |
| title_sort | dna sequence design for molecular computation of hamiltonian path problem with output visualization based on real-time pcr |
| topic | TK Electrical engineering. Electronics Nuclear engineering |
| url | http://eprints.utm.my/9927/ http://eprints.utm.my/9927/ http://eprints.utm.my/9927/1/ZuwairieIbrahim2008_ADNASequenceDesignForMplecularComputation.pdf |