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Evaluation of ordering methods for DNA sequence design based on ant colony system

Hybridization between a DNA sequence and its base-pairing complement is crucial in DNA computing to retrieve the information stored in DNA sequences and operate a computation processes. Therefore, much works have focused on designing the DNA sequences for a reliable molecular computation. In this pa...

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Main Authors:	Kurniawan, Tri Basuki, Khalid, Noor Khafifah, Ibrahim, Zuwairie, Khalid, Marzuki, Middendorf, Martin
Format:	Book Section
Published:	Institute of Electrical and Electronics Engineers 2008
Subjects:	TK Electrical engineering. Electronics Nuclear engineering
Online Access:	http://eprints.utm.my/id/eprint/12558/ http://dx.doi.org/10.1109/AMS.2008.37
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id	my.utm.12558
record_format	eprints
spelling	my.utm.125582017-10-02T08:48:05Z http://eprints.utm.my/id/eprint/12558/ Evaluation of ordering methods for DNA sequence design based on ant colony system Kurniawan, Tri Basuki Khalid, Noor Khafifah Ibrahim, Zuwairie Khalid, Marzuki Middendorf, Martin TK Electrical engineering. Electronics Nuclear engineering Hybridization between a DNA sequence and its base-pairing complement is crucial in DNA computing to retrieve the information stored in DNA sequences and operate a computation processes. Therefore, much works have focused on designing the DNA sequences for a reliable molecular computation. In this paper, Ant Colony System (ACS) is proposed to solve the DNA sequence design problem. ACS, which is based on Ant Colony Optimization (ACO) is an improvement of Ant System (AS) that uses some agents to obtain the solutions based on the pheromone in their colony. The DNA sequence design problem is modeled by four nodes, representing four DNA bases (A, T, C, and G) using the nearest-neighbor thermodynamic parameter's Watson-Crick base-pair ?G°37 as distances between one node to other nodes. Seven ordering methods for ACS are presented in this study in order to obtain the best set solution. The performance of each of those methods are compared and evaluated to decide the best ordering method for this application. Institute of Electrical and Electronics Engineers 2008 Book Section PeerReviewed Kurniawan, Tri Basuki and Khalid, Noor Khafifah and Ibrahim, Zuwairie and Khalid, Marzuki and Middendorf, Martin (2008) Evaluation of ordering methods for DNA sequence design based on ant colony system. In: Proceedings - 2nd Asia International Conference on Modelling and Simulation, AMS 2008. Institute of Electrical and Electronics Engineers, New York, 905 -910. ISBN 978-076953136-6 http://dx.doi.org/10.1109/AMS.2008.37 DOI:10.1109/AMS.2008.37
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 Kurniawan, Tri Basuki Khalid, Noor Khafifah Ibrahim, Zuwairie Khalid, Marzuki Middendorf, Martin Evaluation of ordering methods for DNA sequence design based on ant colony system
description	Hybridization between a DNA sequence and its base-pairing complement is crucial in DNA computing to retrieve the information stored in DNA sequences and operate a computation processes. Therefore, much works have focused on designing the DNA sequences for a reliable molecular computation. In this paper, Ant Colony System (ACS) is proposed to solve the DNA sequence design problem. ACS, which is based on Ant Colony Optimization (ACO) is an improvement of Ant System (AS) that uses some agents to obtain the solutions based on the pheromone in their colony. The DNA sequence design problem is modeled by four nodes, representing four DNA bases (A, T, C, and G) using the nearest-neighbor thermodynamic parameter's Watson-Crick base-pair ?G°37 as distances between one node to other nodes. Seven ordering methods for ACS are presented in this study in order to obtain the best set solution. The performance of each of those methods are compared and evaluated to decide the best ordering method for this application.
format	Book Section
author	Kurniawan, Tri Basuki Khalid, Noor Khafifah Ibrahim, Zuwairie Khalid, Marzuki Middendorf, Martin
author_facet	Kurniawan, Tri Basuki Khalid, Noor Khafifah Ibrahim, Zuwairie Khalid, Marzuki Middendorf, Martin
author_sort	Kurniawan, Tri Basuki
title	Evaluation of ordering methods for DNA sequence design based on ant colony system
title_short	Evaluation of ordering methods for DNA sequence design based on ant colony system
title_full	Evaluation of ordering methods for DNA sequence design based on ant colony system
title_fullStr	Evaluation of ordering methods for DNA sequence design based on ant colony system
title_full_unstemmed	Evaluation of ordering methods for DNA sequence design based on ant colony system
title_sort	evaluation of ordering methods for dna sequence design based on ant colony system
publisher	Institute of Electrical and Electronics Engineers
publishDate	2008
url	http://eprints.utm.my/id/eprint/12558/ http://dx.doi.org/10.1109/AMS.2008.37
_version_	1643645985590607872
score	13.211869

Evaluation of ordering methods for DNA sequence design based on ant colony system

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