A Framework for Reproducible Parallel DNA String Matching

Ricardo Regis Cavalcante Chaves, Alba Cristina Magalhaes Alves de Melo

2025

Abstract

In this paper, we propose an output reproducible framework that executes parallel sequence comparison algorithms, computing the edit distance. The framework generates tables/graphics and linear regressions that can be used to predict the execution times. We also propose parallel OpenMP versions of serial algorithms (DP and UK) used to compute the edit distance. Our parallel DP is antidiagonal block-based, where the blocks that belong to the same set of antidiagonals are assigned to different threads, which compute them simultaneously. Due to data dependencies presented by UK, we opted to compute each antidiagonal in parallel. Our results with synthetic and real sequences show that the parallel UK version presents the best execution times in most cases. We also show that the linear regressions generated by our tool have errors below 10%, on average.

Paper Citation

in Harvard Style

Chaves R. and Alves de Melo A. (2025). A Framework for Reproducible Parallel DNA String Matching. In Proceedings of the 18th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 1: BIOINFORMATICS; ISBN 978-989-758-731-3, SciTePress, pages 661-668. DOI: 10.5220/0013302600003911

in Bibtex Style

@conference{bioinformatics25,
author={Ricardo Chaves and Alba Alves de Melo},
title={A Framework for Reproducible Parallel DNA String Matching},
booktitle={Proceedings of the 18th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 1: BIOINFORMATICS},
year={2025},
pages={661-668},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0013302600003911},
isbn={978-989-758-731-3},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 18th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 1: BIOINFORMATICS
TI - A Framework for Reproducible Parallel DNA String Matching
SN - 978-989-758-731-3
AU - Chaves R.
AU - Alves de Melo A.
PY - 2025
SP - 661
EP - 668
DO - 10.5220/0013302600003911
PB - SciTePress