A Study of the Contribution of Nearest-Neighbour Thermodynamic Parameters to the DNA Sequences Generated by Ant Colony Optimisation
The process of designing a set of good DNA sequences is an essential problem and one of the most practical and important research topics in DNA-based computing and the DNA nanotechnology area. In this field of research, a DNA sequence design problem is defined as a multi-objective problem, and it is...
| Main Authors: | , , , , , , , , , |
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| Format: | Conference or Workshop Item |
| Language: | English |
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2013
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| Subjects: | |
| Online Access: | http://umpir.ump.edu.my/id/eprint/5675/1/Paper_ICMIC_Published_Falfazli.pdf |
| _version_ | 1796989991473119232 |
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| author | Mohd Zaidi, Mohd Tumari Zuwairie, Ibrahim Kamarul Hawari, Ghazali Faradila, Naim Mohd Falfazli, Mat Jusof Ismail, Ibrahim Zulkifli, Md. Yusof Kamal, Khalil Muhammad Arif, Abdul Rahim Sophan Wahyudi, Nawawi |
| author_facet | Mohd Zaidi, Mohd Tumari Zuwairie, Ibrahim Kamarul Hawari, Ghazali Faradila, Naim Mohd Falfazli, Mat Jusof Ismail, Ibrahim Zulkifli, Md. Yusof Kamal, Khalil Muhammad Arif, Abdul Rahim Sophan Wahyudi, Nawawi |
| author_sort | Mohd Zaidi, Mohd Tumari |
| collection | UMP |
| description | The process of designing a set of good DNA sequences is an essential problem and one of the most practical and important research topics in DNA-based computing and the DNA nanotechnology area. In this field of research, a DNA sequence design problem is defined as a multi-objective problem, and it is evaluated using four objective functions, h-measure, similarity, continuity and hairpin. In addition, two constraints, GC content and melting temperature (Tm), are used to maintain uniform chemical characteristics of the sequences. In the authors’ previous research, an ant colony system (ACS) was proposed to solve the DNA sequence design problem based on nearest neighbour. The Watson-Crick base pair ∆Go37 was used as the distance between nodes for the thermodynamic parameters in the problem models for the heuristic approach in the ACS algorithms. In the current study, a non-heuristic approach and four new models using the heuristic approach are proposed, and results from the models are compared. |
| first_indexed | 2024-03-06T11:45:08Z |
| format | Conference or Workshop Item |
| id | UMPir5675 |
| institution | Universiti Malaysia Pahang |
| language | English |
| last_indexed | 2024-03-06T11:45:08Z |
| publishDate | 2013 |
| record_format | dspace |
| spelling | UMPir56752018-02-21T01:57:26Z http://umpir.ump.edu.my/id/eprint/5675/ A Study of the Contribution of Nearest-Neighbour Thermodynamic Parameters to the DNA Sequences Generated by Ant Colony Optimisation Mohd Zaidi, Mohd Tumari Zuwairie, Ibrahim Kamarul Hawari, Ghazali Faradila, Naim Mohd Falfazli, Mat Jusof Ismail, Ibrahim Zulkifli, Md. Yusof Kamal, Khalil Muhammad Arif, Abdul Rahim Sophan Wahyudi, Nawawi TK Electrical engineering. Electronics Nuclear engineering The process of designing a set of good DNA sequences is an essential problem and one of the most practical and important research topics in DNA-based computing and the DNA nanotechnology area. In this field of research, a DNA sequence design problem is defined as a multi-objective problem, and it is evaluated using four objective functions, h-measure, similarity, continuity and hairpin. In addition, two constraints, GC content and melting temperature (Tm), are used to maintain uniform chemical characteristics of the sequences. In the authors’ previous research, an ant colony system (ACS) was proposed to solve the DNA sequence design problem based on nearest neighbour. The Watson-Crick base pair ∆Go37 was used as the distance between nodes for the thermodynamic parameters in the problem models for the heuristic approach in the ACS algorithms. In the current study, a non-heuristic approach and four new models using the heuristic approach are proposed, and results from the models are compared. 2013 Conference or Workshop Item PeerReviewed application/pdf en http://umpir.ump.edu.my/id/eprint/5675/1/Paper_ICMIC_Published_Falfazli.pdf Mohd Zaidi, Mohd Tumari and Zuwairie, Ibrahim and Kamarul Hawari, Ghazali and Faradila, Naim and Mohd Falfazli, Mat Jusof and Ismail, Ibrahim and Zulkifli, Md. Yusof and Kamal, Khalil and Muhammad Arif, Abdul Rahim and Sophan Wahyudi, Nawawi (2013) A Study of the Contribution of Nearest-Neighbour Thermodynamic Parameters to the DNA Sequences Generated by Ant Colony Optimisation. In: International Conference of Modelling Identification and Control (ICMIC2013) , 31 August - 2 September 2013 , Cairo, Egypt. pp. 287-291.. |
| spellingShingle | TK Electrical engineering. Electronics Nuclear engineering Mohd Zaidi, Mohd Tumari Zuwairie, Ibrahim Kamarul Hawari, Ghazali Faradila, Naim Mohd Falfazli, Mat Jusof Ismail, Ibrahim Zulkifli, Md. Yusof Kamal, Khalil Muhammad Arif, Abdul Rahim Sophan Wahyudi, Nawawi A Study of the Contribution of Nearest-Neighbour Thermodynamic Parameters to the DNA Sequences Generated by Ant Colony Optimisation |
| title | A Study of the Contribution of Nearest-Neighbour Thermodynamic Parameters to the DNA Sequences Generated by Ant Colony
Optimisation |
| title_full | A Study of the Contribution of Nearest-Neighbour Thermodynamic Parameters to the DNA Sequences Generated by Ant Colony
Optimisation |
| title_fullStr | A Study of the Contribution of Nearest-Neighbour Thermodynamic Parameters to the DNA Sequences Generated by Ant Colony
Optimisation |
| title_full_unstemmed | A Study of the Contribution of Nearest-Neighbour Thermodynamic Parameters to the DNA Sequences Generated by Ant Colony
Optimisation |
| title_short | A Study of the Contribution of Nearest-Neighbour Thermodynamic Parameters to the DNA Sequences Generated by Ant Colony
Optimisation |
| title_sort | study of the contribution of nearest neighbour thermodynamic parameters to the dna sequences generated by ant colony optimisation |
| topic | TK Electrical engineering. Electronics Nuclear engineering |
| url | http://umpir.ump.edu.my/id/eprint/5675/1/Paper_ICMIC_Published_Falfazli.pdf |
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