Algorithms for Fast and Efficient Sequence Alignment

Valeriy Titarenko, Sofya Titarenko

2025

Abstract

Aligning short sequences against long reference genomes is a challenging task in bioinformatics, particularly when working with the human reference genome. The difficulty increases further when addressing metage-nomic problems or dealing with damaged sequences. One way to enhance efficiency in this process is by using spaced seeds to identify potential alignment locations. Hashing is a foundational technique in many sequence alignment software applications, and improving the speed of hashing can significantly boost the computational efficiency of sequence alignment. Many hashing strategies were developed decades ago, and with recent advances in hardware, it is necessary to reevaluate these approaches. Our research aims to develop optimal tools for sequence alignment that leverage the latest hardware advancements. In this work, we will introduce a new fast hashing strategy focused on optimal data storage, which minimizes the number of logical and bit-shifting SIMD operations required. We will also profile these algorithms against existing sequence alignment tools.

Paper Citation

in Harvard Style

Titarenko V. and Titarenko S. (2025). Algorithms for Fast and Efficient Sequence Alignment. 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 619-626. DOI: 10.5220/0013239800003911

in Bibtex Style

@conference{bioinformatics25,
author={Valeriy Titarenko and Sofya Titarenko},
title={Algorithms for Fast and Efficient Sequence Alignment},
booktitle={Proceedings of the 18th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 1: BIOINFORMATICS},
year={2025},
pages={619-626},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0013239800003911},
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 - Algorithms for Fast and Efficient Sequence Alignment
SN - 978-989-758-731-3
AU - Titarenko V.
AU - Titarenko S.
PY - 2025
SP - 619
EP - 626
DO - 10.5220/0013239800003911
PB - SciTePress