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DNA sequence design for DNA computation based on binary 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 com- putation in vitro, which consists of several chemical rea...

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Main Authors: Ibrahim, Zuwairie, Khalid, Noor Khafifah, Buyamin, Salinda, Ibrahim, Ismail, Ahmed Mukred, Jameel Abdulla, Md. Yusof, Zulkifli, Mohamad, Mohd. Saberi, Mokhtar, N., Mohamed Saaid, Muhammad Faiz, Engelbrecht, Andries
Format: Article
Published: ICIC International 2012
Subjects:
TK Electrical engineering. Electronics Nuclear engineering
Online Access:http://eprints.utm.my/id/eprint/33308/
http://works.bepress.com/mokhtar_norrima/3/
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spelling my.utm.333082017-02-14T07:27:18Z http://eprints.utm.my/id/eprint/33308/ DNA sequence design for DNA computation based on binary particle swarm optimization Ibrahim, Zuwairie Khalid, Noor Khafifah Buyamin, Salinda Ibrahim, Ismail Ahmed Mukred, Jameel Abdulla Md. Yusof, Zulkifli Mohamad, Mohd. Saberi Mokhtar, N. Mohamed Saaid, Muhammad Faiz Engelbrecht, Andries 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 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. ICIC International 2012-05 Article PeerReviewed 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 http://works.bepress.com/mokhtar_norrima/3/
institution Universiti Teknologi Malaysia
building UTM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Teknologi Malaysia
content_source UTM Institutional Repository
url_provider http://eprints.utm.my/
topic TK Electrical engineering. Electronics Nuclear engineering
spellingShingle TK Electrical engineering. Electronics Nuclear engineering
Ibrahim, Zuwairie
Khalid, Noor Khafifah
Buyamin, Salinda
Ibrahim, Ismail
Ahmed Mukred, Jameel Abdulla
Md. Yusof, Zulkifli
Mohamad, Mohd. Saberi
Mokhtar, N.
Mohamed Saaid, Muhammad Faiz
Engelbrecht, Andries
DNA sequence design for DNA computation based on binary 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 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.
format Article
author Ibrahim, Zuwairie
Khalid, Noor Khafifah
Buyamin, Salinda
Ibrahim, Ismail
Ahmed Mukred, Jameel Abdulla
Md. Yusof, Zulkifli
Mohamad, Mohd. Saberi
Mokhtar, N.
Mohamed Saaid, Muhammad Faiz
Engelbrecht, Andries
author_facet Ibrahim, Zuwairie
Khalid, Noor Khafifah
Buyamin, Salinda
Ibrahim, Ismail
Ahmed Mukred, Jameel Abdulla
Md. Yusof, Zulkifli
Mohamad, Mohd. Saberi
Mokhtar, N.
Mohamed Saaid, Muhammad Faiz
Engelbrecht, Andries
author_sort Ibrahim, Zuwairie
title DNA sequence design for DNA computation based on binary particle swarm optimization
title_short DNA sequence design for DNA computation based on binary particle swarm optimization
title_full DNA sequence design for DNA computation based on binary particle swarm optimization
title_fullStr DNA sequence design for DNA computation based on binary particle swarm optimization
title_full_unstemmed DNA sequence design for DNA computation based on binary particle swarm optimization
title_sort dna sequence design for dna computation based on binary particle swarm optimization
publisher ICIC International
publishDate 2012
url http://eprints.utm.my/id/eprint/33308/
http://works.bepress.com/mokhtar_norrima/3/
_version_ 1643649292605325312
score 13.211869

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