IWO Algorithm Based on Niche Crowding for DNA Sequence Design
The design of DNA sequences is essential for the implementation of DNA computing, where the quantity and quality can directly affect the accuracy and efficiency of calculations. Many studies have focused on the design of good DNA sequences to make DNA computing more reliable. However, DNA sequence d...
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| Veröffentlicht in: | Interdisciplinary sciences : computational life sciences 2017-09, Vol.9 (3), p.341-349 |
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| creator | Yang, Gaijing Wang, Bin Zheng, Xuedong Zhou, Changjun Zhang, Qiang |
| description | The design of DNA sequences is essential for the implementation of DNA computing, where the quantity and quality can directly affect the accuracy and efficiency of calculations. Many studies have focused on the design of good DNA sequences to make DNA computing more reliable. However, DNA sequence design needs to satisfy various constraints at the same time, which is an NP-hard problem. In this study, we specify appropriate constraints that should be satisfied in the design of DNA sequences and we propose evaluation formulae. We employ the Invasive Weed Optimization (IWO) algorithm and the niche crowding in the algorithm to solve the DNA sequence design problem. We also improve the spatial dispersal in the traditional IWO algorithm. Finally, we compared the sequences obtained with existing sequences based on the results obtained using a comprehensive fitness function, which demonstrated the efficiency of the proposed method. |
| doi_str_mv | 10.1007/s12539-016-0160-0 |
| format | Article |
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Many studies have focused on the design of good DNA sequences to make DNA computing more reliable. However, DNA sequence design needs to satisfy various constraints at the same time, which is an NP-hard problem. In this study, we specify appropriate constraints that should be satisfied in the design of DNA sequences and we propose evaluation formulae. We employ the Invasive Weed Optimization (IWO) algorithm and the niche crowding in the algorithm to solve the DNA sequence design problem. We also improve the spatial dispersal in the traditional IWO algorithm. Finally, we compared the sequences obtained with existing sequences based on the results obtained using a comprehensive fitness function, which demonstrated the efficiency of the proposed method.</description><identifier>ISSN: 1913-2751</identifier><identifier>EISSN: 1867-1462</identifier><identifier>DOI: 10.1007/s12539-016-0160-0</identifier><identifier>PMID: 27013509</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Algorithms ; Base Sequence ; Biomedical and Life Sciences ; Computational Biology/Bioinformatics ; Computational Science and Engineering ; Computer Appl. in Life Sciences ; Computer Simulation ; Computing time ; Crowding ; Deoxyribonucleic acid ; Design ; Dispersal ; DNA ; Fitness ; Gene sequencing ; Health Sciences ; Invasive plants ; Life Sciences ; Mathematical and Computational Physics ; Medicine ; Nucleotide sequence ; Original Research Article ; Sequence Analysis, DNA ; Statistics for Life Sciences ; Theoretical ; Theoretical and Computational Chemistry</subject><ispartof>Interdisciplinary sciences : computational life sciences, 2017-09, Vol.9 (3), p.341-349</ispartof><rights>International Association of Scientists in the Interdisciplinary Areas and Springer-Verlag Berlin Heidelberg 2016</rights><rights>Interdisciplinary Sciences: Computational Life Sciences is a copyright of Springer, (2016). All Rights Reserved.</rights><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c372t-7efd2bcbeec5673f69bdaf0b08daed863fd8ace725c351f8f7fe59001973a7503</citedby><cites>FETCH-LOGICAL-c372t-7efd2bcbeec5673f69bdaf0b08daed863fd8ace725c351f8f7fe59001973a7503</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s12539-016-0160-0$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s12539-016-0160-0$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27013509$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Yang, Gaijing</creatorcontrib><creatorcontrib>Wang, Bin</creatorcontrib><creatorcontrib>Zheng, Xuedong</creatorcontrib><creatorcontrib>Zhou, Changjun</creatorcontrib><creatorcontrib>Zhang, Qiang</creatorcontrib><title>IWO Algorithm Based on Niche Crowding for DNA Sequence Design</title><title>Interdisciplinary sciences : computational life sciences</title><addtitle>Interdiscip Sci Comput Life Sci</addtitle><addtitle>Interdiscip Sci</addtitle><description>The design of DNA sequences is essential for the implementation of DNA computing, where the quantity and quality can directly affect the accuracy and efficiency of calculations. Many studies have focused on the design of good DNA sequences to make DNA computing more reliable. However, DNA sequence design needs to satisfy various constraints at the same time, which is an NP-hard problem. In this study, we specify appropriate constraints that should be satisfied in the design of DNA sequences and we propose evaluation formulae. We employ the Invasive Weed Optimization (IWO) algorithm and the niche crowding in the algorithm to solve the DNA sequence design problem. We also improve the spatial dispersal in the traditional IWO algorithm. Finally, we compared the sequences obtained with existing sequences based on the results obtained using a comprehensive fitness function, which demonstrated the efficiency of the proposed method.</description><subject>Algorithms</subject><subject>Base Sequence</subject><subject>Biomedical and Life Sciences</subject><subject>Computational Biology/Bioinformatics</subject><subject>Computational Science and Engineering</subject><subject>Computer Appl. in Life Sciences</subject><subject>Computer Simulation</subject><subject>Computing time</subject><subject>Crowding</subject><subject>Deoxyribonucleic acid</subject><subject>Design</subject><subject>Dispersal</subject><subject>DNA</subject><subject>Fitness</subject><subject>Gene sequencing</subject><subject>Health Sciences</subject><subject>Invasive plants</subject><subject>Life Sciences</subject><subject>Mathematical and Computational Physics</subject><subject>Medicine</subject><subject>Nucleotide sequence</subject><subject>Original Research 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Algorithm Based on Niche Crowding for DNA Sequence Design</title><author>Yang, Gaijing ; Wang, Bin ; Zheng, Xuedong ; Zhou, Changjun ; Zhang, Qiang</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c372t-7efd2bcbeec5673f69bdaf0b08daed863fd8ace725c351f8f7fe59001973a7503</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Algorithms</topic><topic>Base Sequence</topic><topic>Biomedical and Life Sciences</topic><topic>Computational Biology/Bioinformatics</topic><topic>Computational Science and Engineering</topic><topic>Computer Appl. in Life Sciences</topic><topic>Computer Simulation</topic><topic>Computing time</topic><topic>Crowding</topic><topic>Deoxyribonucleic acid</topic><topic>Design</topic><topic>Dispersal</topic><topic>DNA</topic><topic>Fitness</topic><topic>Gene sequencing</topic><topic>Health Sciences</topic><topic>Invasive plants</topic><topic>Life 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| source | MEDLINE; SpringerLink Journals |
| subjects | Algorithms Base Sequence Biomedical and Life Sciences Computational Biology/Bioinformatics Computational Science and Engineering Computer Appl. in Life Sciences Computer Simulation Computing time Crowding Deoxyribonucleic acid Design Dispersal DNA Fitness Gene sequencing Health Sciences Invasive plants Life Sciences Mathematical and Computational Physics Medicine Nucleotide sequence Original Research Article Sequence Analysis, DNA Statistics for Life Sciences Theoretical Theoretical and Computational Chemistry |
| title | IWO Algorithm Based on Niche Crowding for DNA Sequence Design |
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