Performance improvement of SNP Search using multithread programming

Detalhes bibliográficos
Autor(a) principal: Zafalon, Geraldo Francisco Donegá [UNESP]
Data de Publicação: 2018
Outros Autores: da Cruz, Álvaro Magri Nogueira [UNESP], Amorim, Anderson Rici [UNESP], Andrade, Matheus Carreira [UNESP], Contessoto, Allan de Godoi [UNESP], Neves, Laendro Alves [UNESP], Souza, Rogéria Cristiane Gratãode [UNESP], Valêncio, Carlos Roberto [UNESP], Sato, Liria Matsumoto
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://dx.doi.org/10.3844/jcssp.2018.1465.1474
http://hdl.handle.net/11449/188571
Resumo: Pattern recognition is an important field in Bioinformatics and a well-known task is the search for Single Nucleotide Polymorphism (SNP). It is possible to search for a known SNP position and analyze it using patterns of DNA bases, called masks. Nonetheless, this process becomes computationally expensive as the amount of available genomic data increases. Thus, in this study, we have developed a parallelization scheme, based on multithread programming, to SNP analysis using masks. In our tests, we noticed that the proposed scheme improved the execution time in 98.05 times when compared with the sequential approach.
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spelling Performance improvement of SNP Search using multithread programmingBioinformaticsMultithreaded approachSNP analysisPattern recognition is an important field in Bioinformatics and a well-known task is the search for Single Nucleotide Polymorphism (SNP). It is possible to search for a known SNP position and analyze it using patterns of DNA bases, called masks. Nonetheless, this process becomes computationally expensive as the amount of available genomic data increases. Thus, in this study, we have developed a parallelization scheme, based on multithread programming, to SNP analysis using masks. In our tests, we noticed that the proposed scheme improved the execution time in 98.05 times when compared with the sequential approach.Centers for Disease Control and PreventionDepartment of Computer Science and Statistics - DCCE São Paulo State University (Unesp) Institute of Biosciences Humanities and Exact Sciences (Ibilce) Campus São José do Rio PretoUniversidade Paulista - ICET Campus de São José do Rio PretoEscola Politécnica University of São PauloDepartment of Computer Science and Statistics - DCCE São Paulo State University (Unesp) Institute of Biosciences Humanities and Exact Sciences (Ibilce) Campus São José do Rio PretoCenters for Disease Control and Prevention: 7-02-1053/2017Universidade Estadual Paulista (Unesp)Universidade Paulista - ICETUniversidade de São Paulo (USP)Zafalon, Geraldo Francisco Donegá [UNESP]da Cruz, Álvaro Magri Nogueira [UNESP]Amorim, Anderson Rici [UNESP]Andrade, Matheus Carreira [UNESP]Contessoto, Allan de Godoi [UNESP]Neves, Laendro Alves [UNESP]Souza, Rogéria Cristiane Gratãode [UNESP]Valêncio, Carlos Roberto [UNESP]Sato, Liria Matsumoto2019-10-06T16:12:26Z2019-10-06T16:12:26Z2018-01-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article1465-1474http://dx.doi.org/10.3844/jcssp.2018.1465.1474Journal of Computer Science, v. 14, n. 11, p. 1465-1474, 2018.1549-3636http://hdl.handle.net/11449/18857110.3844/jcssp.2018.1465.14742-s2.0-85059518679Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengJournal of Computer Scienceinfo:eu-repo/semantics/openAccess2021-10-23T16:09:06Zoai:repositorio.unesp.br:11449/188571Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-05-23T11:30:12.508490Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Performance improvement of SNP Search using multithread programming
title Performance improvement of SNP Search using multithread programming
spellingShingle Performance improvement of SNP Search using multithread programming
Zafalon, Geraldo Francisco Donegá [UNESP]
Bioinformatics
Multithreaded approach
SNP analysis
title_short Performance improvement of SNP Search using multithread programming
title_full Performance improvement of SNP Search using multithread programming
title_fullStr Performance improvement of SNP Search using multithread programming
title_full_unstemmed Performance improvement of SNP Search using multithread programming
title_sort Performance improvement of SNP Search using multithread programming
author Zafalon, Geraldo Francisco Donegá [UNESP]
author_facet Zafalon, Geraldo Francisco Donegá [UNESP]
da Cruz, Álvaro Magri Nogueira [UNESP]
Amorim, Anderson Rici [UNESP]
Andrade, Matheus Carreira [UNESP]
Contessoto, Allan de Godoi [UNESP]
Neves, Laendro Alves [UNESP]
Souza, Rogéria Cristiane Gratãode [UNESP]
Valêncio, Carlos Roberto [UNESP]
Sato, Liria Matsumoto
author_role author
author2 da Cruz, Álvaro Magri Nogueira [UNESP]
Amorim, Anderson Rici [UNESP]
Andrade, Matheus Carreira [UNESP]
Contessoto, Allan de Godoi [UNESP]
Neves, Laendro Alves [UNESP]
Souza, Rogéria Cristiane Gratãode [UNESP]
Valêncio, Carlos Roberto [UNESP]
Sato, Liria Matsumoto
author2_role author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Universidade Estadual Paulista (Unesp)
Universidade Paulista - ICET
Universidade de São Paulo (USP)
dc.contributor.author.fl_str_mv Zafalon, Geraldo Francisco Donegá [UNESP]
da Cruz, Álvaro Magri Nogueira [UNESP]
Amorim, Anderson Rici [UNESP]
Andrade, Matheus Carreira [UNESP]
Contessoto, Allan de Godoi [UNESP]
Neves, Laendro Alves [UNESP]
Souza, Rogéria Cristiane Gratãode [UNESP]
Valêncio, Carlos Roberto [UNESP]
Sato, Liria Matsumoto
dc.subject.por.fl_str_mv Bioinformatics
Multithreaded approach
SNP analysis
topic Bioinformatics
Multithreaded approach
SNP analysis
description Pattern recognition is an important field in Bioinformatics and a well-known task is the search for Single Nucleotide Polymorphism (SNP). It is possible to search for a known SNP position and analyze it using patterns of DNA bases, called masks. Nonetheless, this process becomes computationally expensive as the amount of available genomic data increases. Thus, in this study, we have developed a parallelization scheme, based on multithread programming, to SNP analysis using masks. In our tests, we noticed that the proposed scheme improved the execution time in 98.05 times when compared with the sequential approach.
publishDate 2018
dc.date.none.fl_str_mv 2018-01-01
2019-10-06T16:12:26Z
2019-10-06T16:12:26Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://dx.doi.org/10.3844/jcssp.2018.1465.1474
Journal of Computer Science, v. 14, n. 11, p. 1465-1474, 2018.
1549-3636
http://hdl.handle.net/11449/188571
10.3844/jcssp.2018.1465.1474
2-s2.0-85059518679
url http://dx.doi.org/10.3844/jcssp.2018.1465.1474
http://hdl.handle.net/11449/188571
identifier_str_mv Journal of Computer Science, v. 14, n. 11, p. 1465-1474, 2018.
1549-3636
10.3844/jcssp.2018.1465.1474
2-s2.0-85059518679
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Journal of Computer Science
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 1465-1474
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
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