DNA sequence design for DNA computation based on binary particle swarm optimization
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Date
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.
Journal Title
Journal ISSN
Volume Title
Publisher
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.
Description
Keywords
Binary PSO, DNA sequence design, Optimization, Deoxyribonucleic acid (DNA), Particle swarm optimization (PSO)
Sustainable Development Goals
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.