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...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Published: |
International Journal of Unconventional Computing
2012
|
| Subjects: |
| _version_ | 1825719200069451776 |
|---|---|
| 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. |
| collection | UM |
| 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. |
| first_indexed | 2024-03-06T05:16:02Z |
| format | Article |
| id | um.eprints-6128 |
| institution | Universiti Malaya |
| last_indexed | 2024-03-06T05:16:02Z |
| publishDate | 2012 |
| publisher | International Journal of Unconventional Computing |
| record_format | dspace |
| spelling | um.eprints-61282013-05-21T02:20:55Z http://eprints.um.edu.my/6128/ 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 Ibrahim, Z. and Khalid, N.K. and Mukred, J.A.A. and Buyamin, S. and Yusof, Z.M. and Saaid, M.F.M. and Mokhtar, N. and Engelbrecht, A.R. (2012) A DNA sequence design for DNA computation based on binary vector evaluated particle swarm optimization. International Journal of Unconventional Computing, 8 (2). pp. 119-137. ISSN 15487199, http://www.scopus.com/inward/record.url?eid=2-s2.0-84862146760&partnerID=40&md5=ccad1c23344f1c3e9a4431a4c1644f71 |
| 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 |
| title | 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_short | 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 |
| topic | TA Engineering (General). Civil engineering (General) TK Electrical engineering. Electronics Nuclear engineering |
| work_keys_str_mv | AT ibrahimz adnasequencedesignfordnacomputationbasedonbinaryvectorevaluatedparticleswarmoptimization AT khalidnk adnasequencedesignfordnacomputationbasedonbinaryvectorevaluatedparticleswarmoptimization AT mukredjaa adnasequencedesignfordnacomputationbasedonbinaryvectorevaluatedparticleswarmoptimization AT buyamins adnasequencedesignfordnacomputationbasedonbinaryvectorevaluatedparticleswarmoptimization AT yusofzm adnasequencedesignfordnacomputationbasedonbinaryvectorevaluatedparticleswarmoptimization AT saaidmfm adnasequencedesignfordnacomputationbasedonbinaryvectorevaluatedparticleswarmoptimization AT mokhtarn adnasequencedesignfordnacomputationbasedonbinaryvectorevaluatedparticleswarmoptimization AT engelbrechtar adnasequencedesignfordnacomputationbasedonbinaryvectorevaluatedparticleswarmoptimization AT ibrahimz dnasequencedesignfordnacomputationbasedonbinaryvectorevaluatedparticleswarmoptimization AT khalidnk dnasequencedesignfordnacomputationbasedonbinaryvectorevaluatedparticleswarmoptimization AT mukredjaa dnasequencedesignfordnacomputationbasedonbinaryvectorevaluatedparticleswarmoptimization AT buyamins dnasequencedesignfordnacomputationbasedonbinaryvectorevaluatedparticleswarmoptimization AT yusofzm dnasequencedesignfordnacomputationbasedonbinaryvectorevaluatedparticleswarmoptimization AT saaidmfm dnasequencedesignfordnacomputationbasedonbinaryvectorevaluatedparticleswarmoptimization AT mokhtarn dnasequencedesignfordnacomputationbasedonbinaryvectorevaluatedparticleswarmoptimization AT engelbrechtar dnasequencedesignfordnacomputationbasedonbinaryvectorevaluatedparticleswarmoptimization |