Journal of Computer Science

Performance Improvement of SNP Search Using Multithread Programming

Geraldo Francisco Donegá Zafalon, Álvaro Magri Nogueira da Cruz, Anderson Rici Amorim, Matheus Carreira Andrade, Allan de Godoi Contessoto, Laendro Alves Neves, Rogéria Cristiane Gratãode Souza, Carlos Roberto Valêncio and Liria Matsumoto Sato

Journal of Computer Science

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.

Copyright

© 2018 Geraldo Francisco Donegá Zafalon, Álvaro Magri Nogueira da Cruz, Anderson Rici Amorim, Matheus Carreira Andrade, Allan de Godoi Contessoto, Laendro Alves Neves, Rogéria Cristiane Gratãode Souza, Carlos Roberto Valêncio and Liria Matsumoto Sato. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.