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Stable DNA Sequence Over Close-Ending and Pairing Sequences Constraint

DNA computing is a new method based on molecular biotechnology to solve complex problems. The design of DNA sequences is a multi-objective optimization problem in DNA computing, whose objective is to obtain optimized sequences that satisfy multiple constraints to improve the quality of the sequences...

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Autores principales: Li, Xue, Wei, Ziqi, Wang, Bin, Song, Tao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8165483/
https://www.ncbi.nlm.nih.gov/pubmed/34079580
http://dx.doi.org/10.3389/fgene.2021.644484
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author Li, Xue
Wei, Ziqi
Wang, Bin
Song, Tao
author_facet Li, Xue
Wei, Ziqi
Wang, Bin
Song, Tao
author_sort Li, Xue
collection PubMed
description DNA computing is a new method based on molecular biotechnology to solve complex problems. The design of DNA sequences is a multi-objective optimization problem in DNA computing, whose objective is to obtain optimized sequences that satisfy multiple constraints to improve the quality of the sequences. However, the previous optimized DNA sequences reacted with each other, which reduced the number of DNA sequences that could be used for molecular hybridization in the solution and thus reduced the accuracy of DNA computing. In addition, a DNA sequence and its complement follow the principle of complementary pairing, and the sequence of base GC at both ends is more stable. To optimize the above problems, the constraints of Pairing Sequences Constraint (PSC) and Close-ending along with the Improved Chaos Whale (ICW) optimization algorithm were proposed to construct a DNA sequence set that satisfies the combination of constraints. The ICW optimization algorithm is added to a new predator–prey strategy and sine and cosine functions under the action of chaos. Compared with other algorithms, among the 23 benchmark functions, the new algorithm obtained the minimum value for one-third of the functions and two-thirds of the current minimum value. The DNA sequences satisfying the constraint combination obtained the minimum of fitness values and had stable and usable structures.
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spelling pubmed-81654832021-06-01 Stable DNA Sequence Over Close-Ending and Pairing Sequences Constraint Li, Xue Wei, Ziqi Wang, Bin Song, Tao Front Genet Genetics DNA computing is a new method based on molecular biotechnology to solve complex problems. The design of DNA sequences is a multi-objective optimization problem in DNA computing, whose objective is to obtain optimized sequences that satisfy multiple constraints to improve the quality of the sequences. However, the previous optimized DNA sequences reacted with each other, which reduced the number of DNA sequences that could be used for molecular hybridization in the solution and thus reduced the accuracy of DNA computing. In addition, a DNA sequence and its complement follow the principle of complementary pairing, and the sequence of base GC at both ends is more stable. To optimize the above problems, the constraints of Pairing Sequences Constraint (PSC) and Close-ending along with the Improved Chaos Whale (ICW) optimization algorithm were proposed to construct a DNA sequence set that satisfies the combination of constraints. The ICW optimization algorithm is added to a new predator–prey strategy and sine and cosine functions under the action of chaos. Compared with other algorithms, among the 23 benchmark functions, the new algorithm obtained the minimum value for one-third of the functions and two-thirds of the current minimum value. The DNA sequences satisfying the constraint combination obtained the minimum of fitness values and had stable and usable structures. Frontiers Media S.A. 2021-05-17 /pmc/articles/PMC8165483/ /pubmed/34079580 http://dx.doi.org/10.3389/fgene.2021.644484 Text en Copyright © 2021 Li, Wei, Wang and Song. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Li, Xue
Wei, Ziqi
Wang, Bin
Song, Tao
Stable DNA Sequence Over Close-Ending and Pairing Sequences Constraint
title Stable DNA Sequence Over Close-Ending and Pairing Sequences Constraint
title_full Stable DNA Sequence Over Close-Ending and Pairing Sequences Constraint
title_fullStr Stable DNA Sequence Over Close-Ending and Pairing Sequences Constraint
title_full_unstemmed Stable DNA Sequence Over Close-Ending and Pairing Sequences Constraint
title_short Stable DNA Sequence Over Close-Ending and Pairing Sequences Constraint
title_sort stable dna sequence over close-ending and pairing sequences constraint
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8165483/
https://www.ncbi.nlm.nih.gov/pubmed/34079580
http://dx.doi.org/10.3389/fgene.2021.644484
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