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DNA sequence design for DNA computation based on binary particle swarm optimization

Ibrahim, Zuwairie and Khalid, Noor Khafifah and Buyamin, Salinda and Ibrahim, Ismail and Ahmed Mukred, Jameel Abdulla and Md. Yusof, Zulkifli and Mohamad, Mohd. Saberi and Mokhtar, N. and Mohamed Saaid, Muhammad Faiz and Engelbrecht, Andries (2012) DNA sequence design for DNA computation based on binary particle swarm optimization. International Journal of Innovative Computing Information and Control, 8 (5(B)). pp. 3441-3450. ISSN 1349-4198

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Official URL: http://works.bepress.com/mokhtar_norrima/3/

Abstract

Deoxyribonucleic Acid (DNA) has certain unique properties such as self- assembly and self-complementary in hybridization, which are important in many DNA- based technologies. DNA computing, for example, uses these properties to realize a com- putation in vitro, which consists of several chemical reactions. Other DNA-based tech- nologies such as DNA-based nanotechnology and polymerase chain reaction also depend on hybridization to assemble nanostructure and to amplify DNA templates, respectively. Hybridization of DNA can be controlled by properly designing DNA sequences. In this paper, sequences are designed such that each sequence uniquely hybridizes to its comple- mentary sequence, but not to any other sequences. Objective functions involved are simi- larity, Hmeasure, continuity, and hairpin. Binary particle swarm optimization (BinPSO) is employed to minimize those objectives subjected to two constraints: melting tempera- ture and GCcontent. It is found that BinPSO can provide a set of good DNA sequences, better than basic PSO algorithm in terms of aggregated fitness value.

Item Type:Article
Additional Information:Indexed by Web of Science
Uncontrolled Keywords:particle swarm optimization, binary PSO, DNA sequence design, opti-mization
Subjects:T Technology > TK Electrical engineering. Electronics Nuclear engineering
Divisions:Electrical Engineering
ID Code:33308
Deposited By:INVALID USER
Deposited On:28 Aug 2013 04:07
Last Modified:14 Feb 2017 07:27

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