A DNA sequence design for DNA computation based on binary vector evaluated particle swarm optimization

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 computation, in vitro, which consists of several chemical reacti...

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Main Authors:	Ibrahim, Z., Khalid, N.K., Mukred, J.A.A., Buyamin, S., Yusof, Z.M., Saaid, M.F.M., Mokhtar, N., Engelbrecht, A.R.
Format:	Article
Published:	International Journal of Unconventional Computing 2012
Subjects:	TA Engineering (General). Civil engineering (General) TK Electrical engineering. Electronics Nuclear engineering
Online Access:	http://www.scopus.com/inward/record.url?eid=2-s2.0-84862146760&partnerID=40&md5=ccad1c23344f1c3e9a4431a4c1644f71 http://www.scopus.com/inward/record.url?eid=2-s2.0-84862146760&partnerID=40&md5=ccad1c23344f1c3e9a4431a4c1644f71

id	um-6128
recordtype	eprints
spelling	um-61282013-05-21T02:20:55Z A DNA sequence design for DNA computation based on binary vector evaluated particle swarm optimization Ibrahim, Z. Khalid, N.K. Mukred, J.A.A. Buyamin, S. Yusof, Z.M. Saaid, M.F.M. Mokhtar, N. Engelbrecht, A.R. TA Engineering (General). Civil engineering (General) TK Electrical engineering. Electronics Nuclear engineering 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 computation, in vitro, which consists of several chemical reactions. Other DNA-based technologies 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 study, sequences are designed such that each sequence uniquely hybridizes to its complementary sequence, but not to any other sequences. This objective can be formulated using four objective functions, namely, similarity, H-measure, continuity, and hairpin. Binary vector evaluated particle swarm optimization (Binary VEPSO) is employed to solve the DNA sequence design problem by minimizing the objective functions subjected to two constraints: melting temperature and GC(content). Several set of good sequences are produced, which are better than other research works where only a set of sequences is generated. International Journal of Unconventional Computing 2012 Article PeerReviewed http://www.scopus.com/inward/record.url?eid=2-s2.0-84862146760&partnerID=40&md5=ccad1c23344f1c3e9a4431a4c1644f71 Ibrahim, Z.; Khalid, N.K.; Mukred, J.A.A.; Buyamin, S.; Yusof, Z.M.; Saaid, M.F.M.; Mokhtar, N.; Engelbrecht, A.R. (2012) A DNA sequence design for DNA computation based on binary vector evaluated particle swarm optimization. International Journal of Unconventional Computing <http://eprints.um.edu.my/view/publication/International_Journal_of_Unconventional_Computing.html>, 8 (2). pp. 119-137. ISSN 15487199 http://eprints.um.edu.my/6128/
repository_type	Digital Repository
institution_category	Local University
institution	University Malaya
building	UM Research Repository
collection	Online Access
topic	TA Engineering (General). Civil engineering (General) TK Electrical engineering. Electronics Nuclear engineering
spellingShingle	TA Engineering (General). Civil engineering (General) TK Electrical engineering. Electronics Nuclear engineering Ibrahim, Z. Khalid, N.K. Mukred, J.A.A. Buyamin, S. Yusof, Z.M. Saaid, M.F.M. Mokhtar, N. Engelbrecht, A.R. A DNA sequence design for DNA computation based on binary vector evaluated particle swarm optimization
description	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 computation, in vitro, which consists of several chemical reactions. Other DNA-based technologies 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 study, sequences are designed such that each sequence uniquely hybridizes to its complementary sequence, but not to any other sequences. This objective can be formulated using four objective functions, namely, similarity, H-measure, continuity, and hairpin. Binary vector evaluated particle swarm optimization (Binary VEPSO) is employed to solve the DNA sequence design problem by minimizing the objective functions subjected to two constraints: melting temperature and GC(content). Several set of good sequences are produced, which are better than other research works where only a set of sequences is generated.
format	Article
author	Ibrahim, Z. Khalid, N.K. Mukred, J.A.A. Buyamin, S. Yusof, Z.M. Saaid, M.F.M. Mokhtar, N. Engelbrecht, A.R.
author_facet	Ibrahim, Z. Khalid, N.K. Mukred, J.A.A. Buyamin, S. Yusof, Z.M. Saaid, M.F.M. Mokhtar, N. Engelbrecht, A.R.
author_sort	Ibrahim, Z.
title	A DNA sequence design for DNA computation based on binary vector evaluated particle swarm optimization
title_short	A DNA sequence design for DNA computation based on binary vector evaluated particle swarm optimization
title_full	A DNA sequence design for DNA computation based on binary vector evaluated particle swarm optimization
title_fullStr	A DNA sequence design for DNA computation based on binary vector evaluated particle swarm optimization
title_full_unstemmed	A DNA sequence design for DNA computation based on binary vector evaluated particle swarm optimization
title_sort	dna sequence design for dna computation based on binary vector evaluated particle swarm optimization
publisher	International Journal of Unconventional Computing
publishDate	2012
url	http://www.scopus.com/inward/record.url?eid=2-s2.0-84862146760&partnerID=40&md5=ccad1c23344f1c3e9a4431a4c1644f71 http://www.scopus.com/inward/record.url?eid=2-s2.0-84862146760&partnerID=40&md5=ccad1c23344f1c3e9a4431a4c1644f71
first_indexed	2018-09-06T05:17:33Z
last_indexed	2018-09-06T05:17:33Z
_version_	1610834042088849408

A DNA sequence design for DNA computation based on binary vector evaluated particle swarm optimization

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