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Research Article · Open access · Published 7 November 2018

Performance Improvement of SNP Search Using Multithread Programming

Geraldo Francisco Donegá Zafalon1, Álvaro Magri Nogueira da Cruz1, Anderson Rici Amorim2, Matheus Carreira Andrade1, Allan de Godoi Contessoto2, Laendro Alves Neves1, Rogéria Cristiane Gratãode Souza1, Carlos Roberto Valêncio1 & Liria Matsumoto Sato2

Journal of Computer Science, Volume 14, Issue 11, pp. 1465–1474 · doi.org/10.3844/jcssp.2018.1465.1474

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Abstract

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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Donegá Zafalon, G. F., Nogueira da Cruz, &. M., Amorim, A. R., Andrade, M. C., Contessoto, A. G., Neves, L. A., Gratãode Souza, R. C., Valêncio, C. R. & Sato, L. M. (2018). Performance Improvement of SNP Search Using Multithread Programming. Journal of Computer Science, 14(11), 1465–1474. https://doi.org/10.3844/jcssp.2018.1465.1474

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Performance Improvement of SNP Search Using Multithread ProgrammingJournal of Computer Science · Volume 14, Issue 11 · pp. 1465–1474 · CC BY 3.0Download