Staff View: A study of the contribution of nearest-neighbour thermodynamic parameters to the DNA sequences generated by ant colony optimisation

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:	Ibrahim, Zuwairie, Ibrahim, Ismail, Mat Jusof, Mohd. Falfazli, Naim, Faradila, Mohd. Tumari, Mohd. Zaidi, Saealal, Muhammad Salihin, Arshad, Nurul Wahidah, Ghazali, Kamarul Hawari, Md. Yusof, Zulkifli, Khalil, Kamal, Abdul Rahim, Muhammad Arif, Abdul Wahab, Norhaliza, Nawawi, Sophan Wahyudi
Format:	Conference or Workshop Item
Published:	2013
Subjects:	TK Electrical engineering. Electronics Nuclear engineering
Online Access:	http://eprints.utm.my/id/eprint/39542/
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id	my.utm.39542
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spelling	my.utm.395422017-09-25T07:58:55Z http://eprints.utm.my/id/eprint/39542/ A study of the contribution of nearest-neighbour thermodynamic parameters to the DNA sequences generated by ant colony optimisation Ibrahim, Zuwairie Ibrahim, Ismail Mat Jusof, Mohd. Falfazli Naim, Faradila Mohd. Tumari, Mohd. Zaidi Saealal, Muhammad Salihin Arshad, Nurul Wahidah Ghazali, Kamarul Hawari Md. Yusof, Zulkifli Khalil, Kamal Abdul Rahim, Muhammad Arif Abdul Wahab, Norhaliza Nawawi, Sophan Wahyudi 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 ΔGo37 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 Ibrahim, Zuwairie and Ibrahim, Ismail and Mat Jusof, Mohd. Falfazli and Naim, Faradila and Mohd. Tumari, Mohd. Zaidi and Saealal, Muhammad Salihin and Arshad, Nurul Wahidah and Ghazali, Kamarul Hawari and Md. Yusof, Zulkifli and Khalil, Kamal and Abdul Rahim, Muhammad Arif and Abdul Wahab, Norhaliza and Nawawi, Sophan Wahyudi (2013) A study of the contribution of nearest-neighbour thermodynamic parameters to the DNA sequences generated by ant colony optimisation. In: The 5th International Conference on Modelling, Identification and Control (ICMIC 2013), 2013.
institution	Universiti Teknologi Malaysia
building	UTM Library
collection	Institutional Repository
continent	Asia
country	Malaysia
content_provider	Universiti Teknologi Malaysia
content_source	UTM Institutional Repository
url_provider	http://eprints.utm.my/
topic	TK Electrical engineering. Electronics Nuclear engineering
spellingShingle	TK Electrical engineering. Electronics Nuclear engineering Ibrahim, Zuwairie Ibrahim, Ismail Mat Jusof, Mohd. Falfazli Naim, Faradila Mohd. Tumari, Mohd. Zaidi Saealal, Muhammad Salihin Arshad, Nurul Wahidah Ghazali, Kamarul Hawari Md. Yusof, Zulkifli Khalil, Kamal Abdul Rahim, Muhammad Arif Abdul Wahab, Norhaliza Nawawi, Sophan Wahyudi 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 ΔGo37 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	Ibrahim, Zuwairie Ibrahim, Ismail Mat Jusof, Mohd. Falfazli Naim, Faradila Mohd. Tumari, Mohd. Zaidi Saealal, Muhammad Salihin Arshad, Nurul Wahidah Ghazali, Kamarul Hawari Md. Yusof, Zulkifli Khalil, Kamal Abdul Rahim, Muhammad Arif Abdul Wahab, Norhaliza Nawawi, Sophan Wahyudi
author_facet	Ibrahim, Zuwairie Ibrahim, Ismail Mat Jusof, Mohd. Falfazli Naim, Faradila Mohd. Tumari, Mohd. Zaidi Saealal, Muhammad Salihin Arshad, Nurul Wahidah Ghazali, Kamarul Hawari Md. Yusof, Zulkifli Khalil, Kamal Abdul Rahim, Muhammad Arif Abdul Wahab, Norhaliza Nawawi, Sophan Wahyudi
author_sort	Ibrahim, Zuwairie
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://eprints.utm.my/id/eprint/39542/
_version_	1643650338969878528
score	13.211869

A study of the contribution of nearest-neighbour thermodynamic parameters to the DNA sequences generated by ant colony optimisation

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