A DNA sequence design for molecular computation of HPP with output visualization based on real-time PCR
Molecular computing has proved its possibility to solve weighted graph problem such as Hamiltonian Path Problem (HPP), Traveling Salesman Problem (TSP) and the Shortest Path Problem (SPP). Normally, in molecular computation, the DNA sequences used for the computation should be critically designed in...
| Main Authors: | , , |
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| Format: | Article |
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2008
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| Online Access: | http://eprints.utm.my/9924/ |
| _version_ | 1848891975955120128 |
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| author | Ibrahim, Zuwairie Kurniawan, Tri Basuki Khalid, Marzuki |
| author_facet | Ibrahim, Zuwairie Kurniawan, Tri Basuki Khalid, Marzuki |
| author_sort | Ibrahim, Zuwairie |
| building | UTeM Institutional Repository |
| collection | Online Access |
| description | Molecular computing has proved its possibility to solve weighted graph problem such as Hamiltonian Path Problem (HPP), Traveling Salesman Problem (TSP) and the Shortest Path Problem (SPP). 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 readout method tailored specifically to HPP in DNA Computing using real-time PCR for output visualization. Six nodes of 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 | 2025-11-15T21:06:31Z |
| format | Article |
| id | utm-9924 |
| institution | Universiti Teknologi Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-15T21:06:31Z |
| publishDate | 2008 |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | utm-99242017-10-23T11:16:40Z http://eprints.utm.my/9924/ A DNA sequence design for molecular computation of HPP with output visualization based on real-time PCR Ibrahim, Zuwairie Kurniawan, Tri Basuki Khalid, Marzuki T Technology (General) TK Electrical engineering. Electronics Nuclear engineering Molecular computing has proved its possibility to solve weighted graph problem such as Hamiltonian Path Problem (HPP), Traveling Salesman Problem (TSP) and the Shortest Path Problem (SPP). 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 readout method tailored specifically to HPP in DNA Computing using real-time PCR for output visualization. Six nodes of 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. 2008 Article PeerReviewed Ibrahim, Zuwairie and Kurniawan, Tri Basuki and Khalid, Marzuki (2008) A DNA sequence design for molecular computation of HPP with output visualization based on real-time PCR. 2007 IEEE Congress on Evolutionary Computation, CEC 2007, 1-10 . pp. 1823-1828. ISSN 0128-4428 http://dx.doi.org/10.1109/CEC.2007.4424694 |
| spellingShingle | T Technology (General) TK Electrical engineering. Electronics Nuclear engineering Ibrahim, Zuwairie Kurniawan, Tri Basuki Khalid, Marzuki A DNA sequence design for molecular computation of HPP with output visualization based on real-time PCR |
| title | A DNA sequence design for molecular computation of HPP with output visualization based on real-time PCR
|
| title_full | A DNA sequence design for molecular computation of HPP with output visualization based on real-time PCR
|
| title_fullStr | A DNA sequence design for molecular computation of HPP with output visualization based on real-time PCR
|
| title_full_unstemmed | A DNA sequence design for molecular computation of HPP with output visualization based on real-time PCR
|
| title_short | A DNA sequence design for molecular computation of HPP with output visualization based on real-time PCR
|
| title_sort | dna sequence design for molecular computation of hpp with output visualization based on real-time pcr |
| topic | T Technology (General) TK Electrical engineering. Electronics Nuclear engineering |
| url | http://eprints.utm.my/9924/ http://eprints.utm.my/9924/ |