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A DNA sequence design approach based on particle swarm optimization with sequence support system

Khalid, Noor Khafifah and Ibrahim, Zuwairie and Kurniawan, Tri Basuki and Khalid, Marzuki and Sudin, Shahdan (2008) A DNA sequence design approach based on particle swarm optimization with sequence support system. In: FEEIIC Symposium on Engineering and Technology 2008, 2008, Kuching, Sarawak.

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Abstract

In DNA based computation and DNA nanotechnology, the design of good DNA sequences has turned out to be an essential problem and one of the most practical and important research topics. Basically, DNA sequence design problem is multi objectives problem, and it can be evaluated using four objective functions, namely, Hmeasure, similarity, continuity, and hairpin. In this paper, this problem is converted into single objective problem, where the weight of each objective is determined systematically using conventional weighted aggregation (CWA). Particle swarm optimization (PSO) is proposed to minimize those objective functions, subjected to two constraints: melting temperature and GCcontent. A model is presented in order to solve DNA sequence design problem based on PSO. To assess the utilization of CWA in the problem, the comparison between CWA and user-defined weights and other existing approach are demonstrated. The implementation of the optimization process is presented using 20 particles and the average values for 20 runs are shown.

Item Type:Conference or Workshop Item (Paper)
Subjects:T Technology > TK Electrical engineering. Electronics Nuclear engineering
Divisions:Electrical Engineering
ID Code:16912
Deposited By: Liza Porijo
Deposited On:09 Nov 2011 08:00
Last Modified:09 Nov 2011 08:02

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