Implementation of Hyyro’s bit-vector algorithm using advanced vector extensions 2
College
College of Computer Studies
Department/Unit
Computer Technology
Document Type
Article
Source Title
International Journal of Advances in Intelligent Informatics
Volume
5
Issue
3
First Page
230
Last Page
242
Publication Date
11-1-2019
Abstract
The Advanced Vector Extensions 2 (AVX2) instruction set architecture was introduced by Intel’s Haswell microarchitecture that features improved processing power, wider vector registers, and a rich instruction set. This study presents an implementation of the Hyyrö’s bit-vector algorithm for pairwise Deoxyribonucleic Acid (DNA) sequence alignment that takes advantage of Single-Instruction-Multiple-Data (SIMD) computing capabilities of AVX2 on modern processors. It investigated the effects of the length of the query and reference sequences to the I/O load time, computation time, and memory consumption. The result reveals that the experiment has achieved an I/O load time of ϴ(n), computation time of ϴ(n*⌈m/64⌉), and memory consumption of ϴ(n). The implementation computed more extended time complexity than the expected ϴ(n) due to instructional and architectural limitations. Nonetheless, it was par with other experiments, in terms of computation time complexity and memory consumption. © 2019, Universitas Ahmad Dahlan. All rights reserved.
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Digitial Object Identifier (DOI)
10.26555/ijain.v5i3.362
Recommended Citation
Chua, K. C., Villamayor, J. F., Bautista, L. C., & Uy, R. (2019). Implementation of Hyyro’s bit-vector algorithm using advanced vector extensions 2. International Journal of Advances in Intelligent Informatics, 5 (3), 230-242. https://doi.org/10.26555/ijain.v5i3.362
Disciplines
Computer Sciences
Keywords
SIMD (Computer architecture); Nucleotide sequence; High performance processors
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