Universiti Teknologi Malaysia Institutional Repository

Function minimization in DNA sequence design based on continuous particle swarm optimization

Ibrahim, Zuwairie and Khalid, Noor Khafifah and Kurniawan, Tri Basuki and Khalid, Marzuki and Sarmin, Nor Haniza and Engelbrecht, Andries Petrus (2009) Function minimization in DNA sequence design based on continuous particle swarm optimization. ICIC Express Letters, 3 (1). pp. 27-32. ISSN 1881803X

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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, the DNA sequence design problem is a multi-objective problem, and it can be evaluated using four objective functions, namely, Hmeasurei similarity, continuity, and hairpin. In this paper, particle swarm optimization (PSO) is proposed to minimize those objective functions, individually, subjected to two constraints: melting temperature, Tm, and GCcontent. A model is presented in order to minimize the objective functions using PSO. An implementation of the optimization process is presented using 20 particles. The results obtained verified that PSO can be used to minimize each objective individually.

Item Type:Article
Uncontrolled Keywords:DNA computing, DNA sequence design, particle swarm optimization
Subjects:Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Divisions:Electrical Engineering
ID Code:14622
Deposited By: Ms Zalinda Shuratman
Deposited On:30 Sep 2011 15:22
Last Modified:30 Sep 2011 15:22

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