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An ant colony system for DNA sequence design based on thermodynamics

Kurniawan, Tri Basuki and Khalid, Noor Khafifah and Ibrahim, Zuwairie and Khalid, Marzuki and Middendorf, Martin (2008) An ant colony system for DNA sequence design based on thermodynamics. In: The 4th IASTEAD International Conference on Advances in Computer Science and Technology (ACST 2008), 2008, Langkawi.

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Abstract

Hybridization between a DNA sequence and its base- pairing complement is crucial to retrieve the information stored in DNA sequences and operate a computation operation in DNA computing. Therefore, much works have focused on designing the DNA sequences to archive a reliable molecular computation and many algorithms have been proposed to obtain a set of good DNA sequences. In this paper, Ant Colony System (ACS) is proposed to solve the DNA sequence design problem. ACS as a derivate from Ant Colony Optimization (ACO) is an improvement from Ant System (AS) that used some agents to get their solutions based on the pheromone in their colony. A model is prepared which consists of four nodes representing four DNA bases using nearest- neighbor thermodynamic parameter’s Watson-Crick base pair ?Go37 as the distance between nodes. The results of the proposed approach are compared with the other methods such as genetic algorithm and evolutionary algorithm.

Item Type:Conference or Workshop Item (Paper)
Uncontrolled Keywords:DNA sequence design, ant colony system (ACS), thermodynamic
Subjects:T Technology > TK Electrical engineering. Electronics Nuclear engineering
Divisions:Electrical Engineering
ID Code:19024
Deposited By: Liza Porijo
Deposited On:29 Nov 2011 08:52
Last Modified:29 Nov 2011 08:52

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