Optimization of SNP Search Based on Masks Using Graphics Processing Unit

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MetadadosDescriçãoIdioma
Autor(es): dc.contributorUniversidade Estadual Paulista (UNESP)-
Autor(es): dc.contributorCenters for Diseases Control and Prevention-
Autor(es): dc.creatorda Cruz, Álvaro Magri Nogueira-
Autor(es): dc.creatorGomes, Vitoria Zanon-
Autor(es): dc.creatorAndrade, Matheus Carreira-
Autor(es): dc.creatorRici Amorim, Anderson-
Autor(es): dc.creatorValêncio, Carlos Roberto-
Autor(es): dc.creatorVaughan, Gilberto-
Autor(es): dc.creatorDonegá Zafalon, Geraldo Francisco-
Data de aceite: dc.date.accessioned2025-08-21T18:47:32Z-
Data de disponibilização: dc.date.available2025-08-21T18:47:32Z-
Data de envio: dc.date.issued2023-07-29-
Data de envio: dc.date.issued2023-07-29-
Data de envio: dc.date.issued2022-12-31-
Fonte completa do material: dc.identifierhttp://dx.doi.org/10.5220/0011841500003467-
Fonte completa do material: dc.identifierhttp://hdl.handle.net/11449/250025-
Fonte: dc.identifier.urihttp://educapes.capes.gov.br/handle/11449/250025-
Descrição: dc.descriptionIn 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.-
Descrição: dc.descriptionDepartment of Computer Science and Statistics Universidade Estadual Paulista (UNESP), Rua Cristóvão Colombo, 2265, Jardim Nazareth, SP-
Descrição: dc.descriptionDivision of Viral Hepatitis Centers for Diseases Control and Prevention-
Descrição: dc.descriptionDepartment of Computer Science and Statistics Universidade Estadual Paulista (UNESP), Rua Cristóvão Colombo, 2265, Jardim Nazareth, SP-
Formato: dc.format134-141-
Idioma: dc.languageen-
Relação: dc.relationInternational Conference on Enterprise Information Systems, ICEIS - Proceedings-
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Palavras-chave: dc.subjectBioinformatics-
Palavras-chave: dc.subjectGraphics Processing Unit-
Palavras-chave: dc.subjectNext Generation Sequencing-
Palavras-chave: dc.subjectParallel Processing-
Palavras-chave: dc.subjectSingle Nucleotide Polymorphism-
Título: dc.titleOptimization of SNP Search Based on Masks Using Graphics Processing Unit-
Tipo de arquivo: dc.typeaula digital-
Aparece nas coleções:Repositório Institucional - Unesp

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