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A biological sub-sequences detection using integrated BA-PSO based on infection propagation mechanism: Case study COVID-19

The longest common consecutive subsequences (LCCS) play a vital role in revealing the biological relationships between DNA/RNA sequences especially the newly discovered ones such as COVID-19. FLAT is a Fragmented local aligner technique which is an accelerated version of the local pairwise sequence...

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Autores principales: Issa, Mohamed, Helmi, Ahmed M., Elsheikh, Ammar H., Abd Elaziz, Mohamed
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier Ltd. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8527645/
https://www.ncbi.nlm.nih.gov/pubmed/34690450
http://dx.doi.org/10.1016/j.eswa.2021.116063
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author Issa, Mohamed
Helmi, Ahmed M.
Elsheikh, Ammar H.
Abd Elaziz, Mohamed
author_facet Issa, Mohamed
Helmi, Ahmed M.
Elsheikh, Ammar H.
Abd Elaziz, Mohamed
author_sort Issa, Mohamed
collection PubMed
description The longest common consecutive subsequences (LCCS) play a vital role in revealing the biological relationships between DNA/RNA sequences especially the newly discovered ones such as COVID-19. FLAT is a Fragmented local aligner technique which is an accelerated version of the local pairwise sequence alignment algorithm based on meta-heuristic algorithms. The performance of FLAT needs to be enhanced since the huge length of biological sequences leads to trapping in local optima. This paper introduces a modified version of FLAT based on improving the performance of the BA algorithm by integration with particle swarm optimization (PSO) algorithm based on a novel infection mechanism. The proposed algorithm, named BPINF, depends on finding the best-explored solution using BA operators which can infect the agents during the exploitation phase using PSO operators to move toward it instead of moving toward the best-exploited solution. Hence, moving the solutions toward the two best solutions increase the diversity of generated solutions and avoids trapping in local optima. The infection can be propagated through the agents where each infected agent can transfer the infection to other non-infected agents which enhances the diversification of generated solutions. FLAT using the proposed technique (BPINF) was validated to detect LCCS between a set of real biological sequences with huge lengths besides COVID-19 and other well-known viruses. The performance of BPINF was compared to the enhanced versions of BA in the literature and the relevant studies of FLAT. It has a preponderance to find the LCCS with the highest percentage (88%) which is better than other state-of-the-art methods.
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spelling pubmed-85276452021-10-20 A biological sub-sequences detection using integrated BA-PSO based on infection propagation mechanism: Case study COVID-19 Issa, Mohamed Helmi, Ahmed M. Elsheikh, Ammar H. Abd Elaziz, Mohamed Expert Syst Appl Article The longest common consecutive subsequences (LCCS) play a vital role in revealing the biological relationships between DNA/RNA sequences especially the newly discovered ones such as COVID-19. FLAT is a Fragmented local aligner technique which is an accelerated version of the local pairwise sequence alignment algorithm based on meta-heuristic algorithms. The performance of FLAT needs to be enhanced since the huge length of biological sequences leads to trapping in local optima. This paper introduces a modified version of FLAT based on improving the performance of the BA algorithm by integration with particle swarm optimization (PSO) algorithm based on a novel infection mechanism. The proposed algorithm, named BPINF, depends on finding the best-explored solution using BA operators which can infect the agents during the exploitation phase using PSO operators to move toward it instead of moving toward the best-exploited solution. Hence, moving the solutions toward the two best solutions increase the diversity of generated solutions and avoids trapping in local optima. The infection can be propagated through the agents where each infected agent can transfer the infection to other non-infected agents which enhances the diversification of generated solutions. FLAT using the proposed technique (BPINF) was validated to detect LCCS between a set of real biological sequences with huge lengths besides COVID-19 and other well-known viruses. The performance of BPINF was compared to the enhanced versions of BA in the literature and the relevant studies of FLAT. It has a preponderance to find the LCCS with the highest percentage (88%) which is better than other state-of-the-art methods. Elsevier Ltd. 2022-03-01 2021-10-20 /pmc/articles/PMC8527645/ /pubmed/34690450 http://dx.doi.org/10.1016/j.eswa.2021.116063 Text en © 2021 Elsevier Ltd. All rights reserved. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Article
Issa, Mohamed
Helmi, Ahmed M.
Elsheikh, Ammar H.
Abd Elaziz, Mohamed
A biological sub-sequences detection using integrated BA-PSO based on infection propagation mechanism: Case study COVID-19
title A biological sub-sequences detection using integrated BA-PSO based on infection propagation mechanism: Case study COVID-19
title_full A biological sub-sequences detection using integrated BA-PSO based on infection propagation mechanism: Case study COVID-19
title_fullStr A biological sub-sequences detection using integrated BA-PSO based on infection propagation mechanism: Case study COVID-19
title_full_unstemmed A biological sub-sequences detection using integrated BA-PSO based on infection propagation mechanism: Case study COVID-19
title_short A biological sub-sequences detection using integrated BA-PSO based on infection propagation mechanism: Case study COVID-19
title_sort biological sub-sequences detection using integrated ba-pso based on infection propagation mechanism: case study covid-19
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8527645/
https://www.ncbi.nlm.nih.gov/pubmed/34690450
http://dx.doi.org/10.1016/j.eswa.2021.116063
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