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...

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Main Authors:	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
Format:	Conference or Workshop Item
Language:	English
Published:	2013
Subjects:	TK Electrical engineering. Electronics Nuclear engineering
Online Access:	http://umpir.ump.edu.my/id/eprint/5675/ http://umpir.ump.edu.my/id/eprint/5675/1/Paper_ICMIC_Published_Falfazli.pdf

id	ump-5675
recordtype	eprints
spelling	ump-56752018-02-21T01:57:26Z 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..
repository_type	Digital Repository
institution_category	Local University
institution	Universiti Malaysia Pahang
building	UMP Institutional Repository
collection	Online Access
language	English
topic	TK Electrical engineering. Electronics Nuclear engineering
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
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.
format	Conference or Workshop Item
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
title	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_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_sort	study of the contribution of nearest-neighbour thermodynamic parameters to the dna sequences generated by ant colony optimisation
publishDate	2013
url	http://umpir.ump.edu.my/id/eprint/5675/ http://umpir.ump.edu.my/id/eprint/5675/1/Paper_ICMIC_Published_Falfazli.pdf
first_indexed	2023-09-18T22:01:03Z
last_indexed	2023-09-18T22:01:03Z
_version_	1777414400573964288

A Study of the Contribution of Nearest-Neighbour Thermodynamic Parameters to the DNA Sequences Generated by Ant Colony Optimisation

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