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

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Authors

Ibrahim, Zuwairie
Khalid, Noor Khafifah
Buyamin, Salinda
Ibrahim, Ismail
Mukred, Jameel Abdulla Ahmed
Yusof, Zulkifli Md.
Mohamad, Mohd Saberi
Mokhtar, N.
Saaid, Muhammad Faiz Mohamed
Engelbrecht, Andries P.

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ICIC International

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.

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Keywords

Binary PSO, DNA sequence design, Optimization, Deoxyribonucleic acid (DNA), Particle swarm optimization (PSO)

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Citation

Ibrahim, Z, Khalid, NK, Buyamin, S, Ibrahim, I, Mukred, JAA, Yusof, ZM, Mohamad, MS, Mokhtar, N, Saaid, MFM & Engelbrecht, A 2012, 'DNA sequence design for DNA computation based on Binary particle swarm optimization', International Journal of Innovative Computing, Information and Control, vol.8, no. 5, pp. 3441-3450.