Research Article Open Access

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 and Liria Matsumoto Sato2
  • 1 São Paulo State University (Unesp), Brazil
  • 2 University of São Paulo, Brazil

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.

Journal of Computer Science
Volume 14 No. 11, 2018, 1465-1474

DOI: https://doi.org/10.3844/jcssp.2018.1465.1474

Submitted On: 30 July 2018 Published On: 7 November 2018

How to Cite: 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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Keywords

  • Multithreaded Approach
  • SNP Analysis
  • Bioinformatics