Hybridization-ligation versus parallel overlap assembly : an experimental comparison of initial pool generation for direct-proportional length-based DNA computing
Previously, direct-proportional length-based DNA computing (DPLB-DNAC) for solving weighted graph problems has been reported. The proposed DPLB-DNAC has been successfully applied to solve the shortest path problem, which is an instance of weighted graph problems. The design and development of DPLB-D...
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| Language: | English |
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IEEE
2006
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| Online Access: | http://eprints.utm.my/1578/ http://eprints.utm.my/1578/1/zuwairie-ieee1.pdf |
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| author | Ibrahim, Zuwairie Tsuboi, Yusei Ono, Osamu |
| author_facet | Ibrahim, Zuwairie Tsuboi, Yusei Ono, Osamu |
| author_sort | Ibrahim, Zuwairie |
| building | UTeM Institutional Repository |
| collection | Online Access |
| description | Previously, direct-proportional length-based DNA computing (DPLB-DNAC) for solving weighted graph problems has been reported. The proposed DPLB-DNAC has been successfully applied to solve the shortest path problem, which is an instance of weighted graph problems. The design and development of DPLB-DNAC is important in order to extend the capability of DNA computing for solving numerical optimization problem. According to DPLB-DNAC, after the initial pool generation, the initial solution is subjected to amplification by polymerase chain reaction and, finally, the output of the computation is visualized by gel electrophoresis. In this paper, however, we give more attention to the initial pool generation of DPLB-DNAC. For this purpose, two kinds of initial pool generation methods, which are generally used for solving weighted graph problems, are evaluated. Those methods are hybridization-ligation and parallel overlap assembly (POA). It is found that for DPLB-DNAC, POA is better than that of the hybridization-ligation method, in terms of population size, generation time, material usage, and efficiency, as supported by the results of actual experiments. |
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| format | Article |
| id | utm-1578 |
| institution | Universiti Teknologi Malaysia |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T20:37:46Z |
| publishDate | 2006 |
| publisher | IEEE |
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| spelling | utm-15782011-05-20T04:18:20Z http://eprints.utm.my/1578/ Hybridization-ligation versus parallel overlap assembly : an experimental comparison of initial pool generation for direct-proportional length-based DNA computing Ibrahim, Zuwairie Tsuboi, Yusei Ono, Osamu TK Electrical engineering. Electronics Nuclear engineering Previously, direct-proportional length-based DNA computing (DPLB-DNAC) for solving weighted graph problems has been reported. The proposed DPLB-DNAC has been successfully applied to solve the shortest path problem, which is an instance of weighted graph problems. The design and development of DPLB-DNAC is important in order to extend the capability of DNA computing for solving numerical optimization problem. According to DPLB-DNAC, after the initial pool generation, the initial solution is subjected to amplification by polymerase chain reaction and, finally, the output of the computation is visualized by gel electrophoresis. In this paper, however, we give more attention to the initial pool generation of DPLB-DNAC. For this purpose, two kinds of initial pool generation methods, which are generally used for solving weighted graph problems, are evaluated. Those methods are hybridization-ligation and parallel overlap assembly (POA). It is found that for DPLB-DNAC, POA is better than that of the hybridization-ligation method, in terms of population size, generation time, material usage, and efficiency, as supported by the results of actual experiments. IEEE 2006-04 Article PeerReviewed application/pdf en http://eprints.utm.my/1578/1/zuwairie-ieee1.pdf Ibrahim, Zuwairie and Tsuboi, Yusei and Ono, Osamu (2006) Hybridization-ligation versus parallel overlap assembly : an experimental comparison of initial pool generation for direct-proportional length-based DNA computing. IEEE Transactions on Nanobioscience, 5 (2). pp. 103-109. http://ieeexplore.ieee.org |
| spellingShingle | TK Electrical engineering. Electronics Nuclear engineering Ibrahim, Zuwairie Tsuboi, Yusei Ono, Osamu Hybridization-ligation versus parallel overlap assembly : an experimental comparison of initial pool generation for direct-proportional length-based DNA computing |
| title | Hybridization-ligation versus parallel overlap assembly : an experimental comparison of initial pool generation for direct-proportional length-based DNA computing |
| title_full | Hybridization-ligation versus parallel overlap assembly : an experimental comparison of initial pool generation for direct-proportional length-based DNA computing |
| title_fullStr | Hybridization-ligation versus parallel overlap assembly : an experimental comparison of initial pool generation for direct-proportional length-based DNA computing |
| title_full_unstemmed | Hybridization-ligation versus parallel overlap assembly : an experimental comparison of initial pool generation for direct-proportional length-based DNA computing |
| title_short | Hybridization-ligation versus parallel overlap assembly : an experimental comparison of initial pool generation for direct-proportional length-based DNA computing |
| title_sort | hybridization-ligation versus parallel overlap assembly : an experimental comparison of initial pool generation for direct-proportional length-based dna computing |
| topic | TK Electrical engineering. Electronics Nuclear engineering |
| url | http://eprints.utm.my/1578/ http://eprints.utm.my/1578/ http://eprints.utm.my/1578/1/zuwairie-ieee1.pdf |