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

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

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Official URL: http://dx.doi.org/10.1109/AMS.2008.37

Abstract

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.

Item Type:Book Section
Additional Information:ISBN: 978-076953136-6; 2nd Asia International Conference on Modelling and Simulation, AMS 2008; Kuala Lumpur; 13 May 2008 through 15 May 2008
Uncontrolled Keywords:alpha particle spectrometers, asset management, computer systems, DNA, genes, genetic programming, nucleic acids, optimization, organic acids, particle spectrometers
Subjects:T Technology > TK Electrical engineering. Electronics Nuclear engineering
Divisions:Electrical Engineering
ID Code:12558
Deposited By: Liza Porijo
Deposited On:08 Jun 2011 08:09
Last Modified:08 Jun 2011 08:09

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