Proceedings of the Workshop on Computation: Theory and Practice (WCTP 2025)

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Accelerating Zhang’s Six-Frame Alignment Algorithm via Hybrid SIMT Wavefront Parallelization on CUDA

Authors
Althea Zyrie Arceta1, *, Antonio Gabriel Mendoza1, Jose Tristan Tan1, Roger Luis Uy1
1Department of Computer Technology, De La Salle University, Manila, Philippines
*Corresponding author. Email: altheazyrie.arceta@gmail.com
Corresponding Author
Althea Zyrie Arceta
Available Online 30 April 2026.
DOI
10.2991/978-94-6239-638-8_20How to use a DOI?
Keywords
Zhang’s six-frame alignment; DNA-Protein alignment; SIMT; CUDA; Parallel Computing; High Performance Computing
Abstract

Zhang’s six-frame Alignment algorithm is a type of sequence alignment used to identify similarities between DNA and protein sequences and has a wide range of applications in bioinformatics. Zhang’s six-frame translates the DNA sequence across all six possible reading frames to specifically account for frameshift errors and variations. Implementing Zhang’s six-frame sequentially can be computationally expensive, particularly when dealing with large datasets. To address the said issue, this study explores a parallel computing approach using NVIDIA’s CUDA programming model to speed up the implementation of Zhang’s six-frame algorithm. Results showed speedups averaging 3.51x up to 6.03x for the Drosophila melanogaster dataset and speedups averaging 3.44x up to 6.44x for the Arabidopsis thaliana dataset when compared to the sequential implementation.

Copyright
© 2026 The Author(s)
Open Access
Open Access This chapter is licensed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/), which permits any noncommercial use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made.

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Volume Title
Proceedings of the Workshop on Computation: Theory and Practice (WCTP 2025)
Series
Atlantis Highlights in Computer Sciences
Publication Date
30 April 2026
ISBN
978-94-6239-638-8
ISSN
2589-4900
DOI
10.2991/978-94-6239-638-8_20How to use a DOI?
Copyright
© 2026 The Author(s)
Open Access
Open Access This chapter is licensed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/), which permits any noncommercial use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made.

Cite this article

risenwbib
TY  - CONF
AU  - Althea Zyrie Arceta
AU  - Antonio Gabriel Mendoza
AU  - Jose Tristan Tan
AU  - Roger Luis Uy
PY  - 2026
DA  - 2026/04/30
TI  - Accelerating Zhang’s Six-Frame Alignment Algorithm via Hybrid SIMT Wavefront Parallelization on CUDA
BT  - Proceedings of the  Workshop on Computation: Theory and Practice (WCTP 2025)
PB  - Atlantis Press
SP  - 403
EP  - 417
SN  - 2589-4900
UR  - https://doi.org/10.2991/978-94-6239-638-8_20
DO  - 10.2991/978-94-6239-638-8_20
ID  - Arceta2026
ER  -