Optimization of SNP Search Based on Masks Using Graphics Processing Unit
Autor(a) principal: | |
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Data de Publicação: | 2023 |
Outros Autores: | , , , , , |
Tipo de documento: | Artigo de conferência |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.5220/0011841500003467 http://hdl.handle.net/11449/250025 |
Resumo: | In the context of bioinformatics one of the most important problems to be solved is the search for simple nucleotide polymorphism (SNP). When we perform the analysis of the files from the next generation sequencing (NGS) the search task for SNPs becomes more prohibitive due to the millions of sequences present on them. CPU multithreaded approaches are not enough when millions of sequences as considered. Then, the use of graphics processing units (GPUs) is a better alternative, because it can operate with hundreds of arithmetic logic units while CPU with no more than tens. Thus, in this work we developed a method to detect SNPs using a mask approach under GPU architecture. In the tests, a speedup of up to 5175.86 was obtained when compared to the multithreaded CPU approach, evaluating from 100,000 to 800,000 sequences using five masks to detect the occurrence of SNPs. |
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Repositório Institucional da UNESP |
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Optimization of SNP Search Based on Masks Using Graphics Processing UnitBioinformaticsGraphics Processing UnitNext Generation SequencingParallel ProcessingSingle Nucleotide PolymorphismIn the context of bioinformatics one of the most important problems to be solved is the search for simple nucleotide polymorphism (SNP). When we perform the analysis of the files from the next generation sequencing (NGS) the search task for SNPs becomes more prohibitive due to the millions of sequences present on them. CPU multithreaded approaches are not enough when millions of sequences as considered. Then, the use of graphics processing units (GPUs) is a better alternative, because it can operate with hundreds of arithmetic logic units while CPU with no more than tens. Thus, in this work we developed a method to detect SNPs using a mask approach under GPU architecture. In the tests, a speedup of up to 5175.86 was obtained when compared to the multithreaded CPU approach, evaluating from 100,000 to 800,000 sequences using five masks to detect the occurrence of SNPs.Department of Computer Science and Statistics Universidade Estadual Paulista (UNESP), Rua Cristóvão Colombo, 2265, Jardim Nazareth, SPDivision of Viral Hepatitis Centers for Diseases Control and PreventionDepartment of Computer Science and Statistics Universidade Estadual Paulista (UNESP), Rua Cristóvão Colombo, 2265, Jardim Nazareth, SPUniversidade Estadual Paulista (UNESP)Centers for Diseases Control and Preventionda Cruz, Álvaro Magri Nogueira [UNESP]Gomes, Vitoria Zanon [UNESP]Andrade, Matheus Carreira [UNESP]Rici Amorim, Anderson [UNESP]Valêncio, Carlos Roberto [UNESP]Vaughan, GilbertoDonegá Zafalon, Geraldo Francisco [UNESP]2023-07-29T16:15:44Z2023-07-29T16:15:44Z2023-01-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/conferenceObject134-141http://dx.doi.org/10.5220/0011841500003467International Conference on Enterprise Information Systems, ICEIS - Proceedings, v. 2, p. 134-141.2184-4992http://hdl.handle.net/11449/25002510.5220/00118415000034672-s2.0-85160866866Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengInternational Conference on Enterprise Information Systems, ICEIS - Proceedingsinfo:eu-repo/semantics/openAccess2023-07-29T16:15:44Zoai:repositorio.unesp.br:11449/250025Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T18:15:52.468327Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Optimization of SNP Search Based on Masks Using Graphics Processing Unit |
title |
Optimization of SNP Search Based on Masks Using Graphics Processing Unit |
spellingShingle |
Optimization of SNP Search Based on Masks Using Graphics Processing Unit da Cruz, Álvaro Magri Nogueira [UNESP] Bioinformatics Graphics Processing Unit Next Generation Sequencing Parallel Processing Single Nucleotide Polymorphism |
title_short |
Optimization of SNP Search Based on Masks Using Graphics Processing Unit |
title_full |
Optimization of SNP Search Based on Masks Using Graphics Processing Unit |
title_fullStr |
Optimization of SNP Search Based on Masks Using Graphics Processing Unit |
title_full_unstemmed |
Optimization of SNP Search Based on Masks Using Graphics Processing Unit |
title_sort |
Optimization of SNP Search Based on Masks Using Graphics Processing Unit |
author |
da Cruz, Álvaro Magri Nogueira [UNESP] |
author_facet |
da Cruz, Álvaro Magri Nogueira [UNESP] Gomes, Vitoria Zanon [UNESP] Andrade, Matheus Carreira [UNESP] Rici Amorim, Anderson [UNESP] Valêncio, Carlos Roberto [UNESP] Vaughan, Gilberto Donegá Zafalon, Geraldo Francisco [UNESP] |
author_role |
author |
author2 |
Gomes, Vitoria Zanon [UNESP] Andrade, Matheus Carreira [UNESP] Rici Amorim, Anderson [UNESP] Valêncio, Carlos Roberto [UNESP] Vaughan, Gilberto Donegá Zafalon, Geraldo Francisco [UNESP] |
author2_role |
author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (UNESP) Centers for Diseases Control and Prevention |
dc.contributor.author.fl_str_mv |
da Cruz, Álvaro Magri Nogueira [UNESP] Gomes, Vitoria Zanon [UNESP] Andrade, Matheus Carreira [UNESP] Rici Amorim, Anderson [UNESP] Valêncio, Carlos Roberto [UNESP] Vaughan, Gilberto Donegá Zafalon, Geraldo Francisco [UNESP] |
dc.subject.por.fl_str_mv |
Bioinformatics Graphics Processing Unit Next Generation Sequencing Parallel Processing Single Nucleotide Polymorphism |
topic |
Bioinformatics Graphics Processing Unit Next Generation Sequencing Parallel Processing Single Nucleotide Polymorphism |
description |
In the context of bioinformatics one of the most important problems to be solved is the search for simple nucleotide polymorphism (SNP). When we perform the analysis of the files from the next generation sequencing (NGS) the search task for SNPs becomes more prohibitive due to the millions of sequences present on them. CPU multithreaded approaches are not enough when millions of sequences as considered. Then, the use of graphics processing units (GPUs) is a better alternative, because it can operate with hundreds of arithmetic logic units while CPU with no more than tens. Thus, in this work we developed a method to detect SNPs using a mask approach under GPU architecture. In the tests, a speedup of up to 5175.86 was obtained when compared to the multithreaded CPU approach, evaluating from 100,000 to 800,000 sequences using five masks to detect the occurrence of SNPs. |
publishDate |
2023 |
dc.date.none.fl_str_mv |
2023-07-29T16:15:44Z 2023-07-29T16:15:44Z 2023-01-01 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/conferenceObject |
format |
conferenceObject |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.5220/0011841500003467 International Conference on Enterprise Information Systems, ICEIS - Proceedings, v. 2, p. 134-141. 2184-4992 http://hdl.handle.net/11449/250025 10.5220/0011841500003467 2-s2.0-85160866866 |
url |
http://dx.doi.org/10.5220/0011841500003467 http://hdl.handle.net/11449/250025 |
identifier_str_mv |
International Conference on Enterprise Information Systems, ICEIS - Proceedings, v. 2, p. 134-141. 2184-4992 10.5220/0011841500003467 2-s2.0-85160866866 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
International Conference on Enterprise Information Systems, ICEIS - Proceedings |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
134-141 |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1808128913366319104 |