Optimization of SNP Search Based on Masks Using Graphics Processing Unit

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dc.contributor.authorda Cruz, Álvaro Magri Nogueira [UNESP]
dc.contributor.authorGomes, Vitoria Zanon [UNESP]
dc.contributor.authorAndrade, Matheus Carreira [UNESP]
dc.contributor.authorRici Amorim, Anderson [UNESP]
dc.contributor.authorValêncio, Carlos Roberto [UNESP]
dc.contributor.authorVaughan, Gilberto
dc.contributor.authorDonegá Zafalon, Geraldo Francisco [UNESP]
dc.contributor.institutionUniversidade Estadual Paulista (UNESP)
dc.contributor.institutionCenters for Diseases Control and Prevention
dc.date.accessioned2023-07-29T16:15:44Z
dc.date.available2023-07-29T16:15:44Z
dc.date.issued2023-01-01
dc.description.abstractIn 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.en
dc.description.affiliationDepartment of Computer Science and Statistics Universidade Estadual Paulista (UNESP), Rua Cristóvão Colombo, 2265, Jardim Nazareth, SP
dc.description.affiliationDivision of Viral Hepatitis Centers for Diseases Control and Prevention
dc.description.affiliationUnespDepartment of Computer Science and Statistics Universidade Estadual Paulista (UNESP), Rua Cristóvão Colombo, 2265, Jardim Nazareth, SP
dc.format.extent134-141
dc.identifierhttp://dx.doi.org/10.5220/0011841500003467
dc.identifier.citationInternational Conference on Enterprise Information Systems, ICEIS - Proceedings, v. 2, p. 134-141.
dc.identifier.doi10.5220/0011841500003467
dc.identifier.issn2184-4992
dc.identifier.scopus2-s2.0-85160866866
dc.identifier.urihttp://hdl.handle.net/11449/250025
dc.language.isoeng
dc.relation.ispartofInternational Conference on Enterprise Information Systems, ICEIS - Proceedings
dc.sourceScopus
dc.subjectBioinformatics
dc.subjectGraphics Processing Unit
dc.subjectNext Generation Sequencing
dc.subjectParallel Processing
dc.subjectSingle Nucleotide Polymorphism
dc.titleOptimization of SNP Search Based on Masks Using Graphics Processing Uniten
dc.typeTrabalho apresentado em evento
unesp.author.orcid0000-0002-7918-0109[1]
unesp.author.orcid0000-0003-4176-566X[2]
unesp.author.orcid0000-0002-1670-266X[3]
unesp.author.orcid0000-0001-7862-7530[4]
unesp.author.orcid0000-0002-9325-3159[5]
unesp.author.orcid0000-0002-7863-3970[6]
unesp.author.orcid0000-0003-2384-011X[7]

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