Parallel overlap assembly for initial pool generation of direct-proportional length-based DNA
In the previous work, in order to overcome the limitation of constant-proportional length-based DNA computing, an alternative approach, which is called directproportional length-based DNA computing for weighted graph problem has been proposed. Based on the proposed approach, the cost of each path i...
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| Format: | Article |
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ICIC International
2005
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| Online Access: | http://eprints.utm.my/9043/ |
| _version_ | 1848891798434349056 |
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| author | Ibrahim, Zuwairie Tsuboi, Yusei Saufee Muhammad, Mohd. Ono, Osamu Khalid, Marzuki |
| author_facet | Ibrahim, Zuwairie Tsuboi, Yusei Saufee Muhammad, Mohd. Ono, Osamu Khalid, Marzuki |
| author_sort | Ibrahim, Zuwairie |
| building | UTeM Institutional Repository |
| collection | Online Access |
| description | In the previous work, in order to overcome the limitation of constant-proportional length-based DNA computing, an alternative approach, which is called directproportional
length-based DNA computing for weighted graph problem has been proposed. Based on the proposed approach, the cost of each path is encoded proportionally to the length of oligonucleotides, or oligos for short. In other words, the longer oligos are employed to encode larger cost and vice versa. During the initial pool generation, the phase where all the combinations are generated in the solution, a method called hybridization/ligation is employed. However, the initial pool generation based on hybridization/ ligation suffers from the biochemical behavior of hybridization because the longer oligos are more likely to hybridize compared to the shorter oligos. In this paper, an efficient method for initial pool generation, which is parallel overlap assembly is studied, examined, and applied. It turns out that the hybridization/ligation method should be replaced with parallel overlap assembly, for a better and efficient initial pool generation
of direct-proportional length-based DNA computing, and our argument is supported by implementing actual experiments. |
| first_indexed | 2025-11-15T21:03:41Z |
| format | Article |
| id | utm-9043 |
| institution | Universiti Teknologi Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-15T21:03:41Z |
| publishDate | 2005 |
| publisher | ICIC International |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | utm-90432018-10-21T04:29:33Z http://eprints.utm.my/9043/ Parallel overlap assembly for initial pool generation of direct-proportional length-based DNA Ibrahim, Zuwairie Tsuboi, Yusei Saufee Muhammad, Mohd. Ono, Osamu Khalid, Marzuki TK Electrical engineering. Electronics Nuclear engineering In the previous work, in order to overcome the limitation of constant-proportional length-based DNA computing, an alternative approach, which is called directproportional length-based DNA computing for weighted graph problem has been proposed. Based on the proposed approach, the cost of each path is encoded proportionally to the length of oligonucleotides, or oligos for short. In other words, the longer oligos are employed to encode larger cost and vice versa. During the initial pool generation, the phase where all the combinations are generated in the solution, a method called hybridization/ligation is employed. However, the initial pool generation based on hybridization/ ligation suffers from the biochemical behavior of hybridization because the longer oligos are more likely to hybridize compared to the shorter oligos. In this paper, an efficient method for initial pool generation, which is parallel overlap assembly is studied, examined, and applied. It turns out that the hybridization/ligation method should be replaced with parallel overlap assembly, for a better and efficient initial pool generation of direct-proportional length-based DNA computing, and our argument is supported by implementing actual experiments. ICIC International 2005 Article PeerReviewed Ibrahim, Zuwairie and Tsuboi, Yusei and Saufee Muhammad, Mohd. and Ono, Osamu and Khalid, Marzuki (2005) Parallel overlap assembly for initial pool generation of direct-proportional length-based DNA. International Journal of Innovative Computing, Information and Control, 1 (2). pp. 261-275. ISSN 1349-4198 http://www.ijicic.org/contents.htm |
| spellingShingle | TK Electrical engineering. Electronics Nuclear engineering Ibrahim, Zuwairie Tsuboi, Yusei Saufee Muhammad, Mohd. Ono, Osamu Khalid, Marzuki Parallel overlap assembly for initial pool generation of direct-proportional length-based DNA |
| title | Parallel overlap assembly for initial pool generation of direct-proportional length-based DNA |
| title_full | Parallel overlap assembly for initial pool generation of direct-proportional length-based DNA |
| title_fullStr | Parallel overlap assembly for initial pool generation of direct-proportional length-based DNA |
| title_full_unstemmed | Parallel overlap assembly for initial pool generation of direct-proportional length-based DNA |
| title_short | Parallel overlap assembly for initial pool generation of direct-proportional length-based DNA |
| title_sort | parallel overlap assembly for initial pool generation of direct-proportional length-based dna |
| topic | TK Electrical engineering. Electronics Nuclear engineering |
| url | http://eprints.utm.my/9043/ http://eprints.utm.my/9043/ |