Optimization of SNP Search Based on Masks Using Graphics Processing Unit

Álvaro Nogueira da Cruz, Vitoria Gomes, Matheus Andrade, Anderson Amorim, Carlos Valêncio, Gilberto Vaughan, Geraldo Zafalon

2023

Abstract

In the context of bioinformatics one of the most important problems to be solved is the search for simple nu- cleotide 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 com- pared to the multithreaded CPU approach, evaluating from 100,000 to 800,000 sequences using five masks to detect the occurrence of SNPs.

Paper Citation

in Harvard Style

Nogueira da Cruz Á., Gomes V., Andrade M., Amorim A., Valêncio C., Vaughan G. and Zafalon G. (2023). Optimization of SNP Search Based on Masks Using Graphics Processing Unit. In Proceedings of the 25th International Conference on Enterprise Information Systems - Volume 2: ICEIS, ISBN 978-989-758-648-4, SciTePress, pages 134-141. DOI: 10.5220/0011841500003467

in Bibtex Style

@conference{iceis23,
author={Álvaro Nogueira da Cruz and Vitoria Gomes and Matheus Andrade and Anderson Amorim and Carlos Valêncio and Gilberto Vaughan and Geraldo Zafalon},
title={Optimization of SNP Search Based on Masks Using Graphics Processing Unit},
booktitle={Proceedings of the 25th International Conference on Enterprise Information Systems - Volume 2: ICEIS,},
year={2023},
pages={134-141},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0011841500003467},
isbn={978-989-758-648-4},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 25th International Conference on Enterprise Information Systems - Volume 2: ICEIS,
TI - Optimization of SNP Search Based on Masks Using Graphics Processing Unit
SN - 978-989-758-648-4
AU - Nogueira da Cruz Á.
AU - Gomes V.
AU - Andrade M.
AU - Amorim A.
AU - Valêncio C.
AU - Vaughan G.
AU - Zafalon G.
PY - 2023
SP - 134
EP - 141
DO - 10.5220/0011841500003467
PB - SciTePress