Work

FORAlign: accelerating gap-affine DNA pairwise sequence alignment using FOR-blocks based on Four Russians approach with linear space complexity

Year: 2024

Type: article

Abstract: Pairwise sequence alignment (PSA) serves as the cornerstone in computational bioinformatics, facilitating multiple sequence alignment and phylogenetic analysis. This paper introduces the FORAlign algorithm, leveraging the Four Russians algorithm with identical upper-bound time and space complexity as the Hirschberg divide-and-conquer PSA algorithm, aimed at accelerating Hirschberg PSA algorithm in parallel. Particularly notable is its capability to achieve up to 16.79 times speedup when aligning sequences with low sequence similarity, compared to the conventional Needleman-Wunsch PSA method using non-heuristic methods. Empirical evaluations underscore FORAlign's superiority over existing wavefront alignment (WFA) series software, especially in scenarios characterized by low sequence similarity during PSA tasks. Our method is capable of directly aligning monkeypox sequences with other sequences using non-heuristic methods. The algorithm was implemented within the FORAlign library, providing functionality for PSA and foundational support for multiple sequence alignment and phylogenetic trees. The FORAlign library is freely available at https://github.com/malabz/FORAlign.

Source: Briefings in Bioinformatics

DOI: 10.1093/bib/bbaf061

Authors: Yanming Wei, Tong Zhou, Yixiao Zhai, Liang Yu, Quan Zou

Institutions: Xidian University, University of Electronic Science and Technology of China

Language: English

Topic: Algorithms and Data Compression

Subfield: Artificial Intelligence

Field: Computer Science

Domain: Physical Sciences

Open Access status: gold

Estimated APC paid: $3,922

Funders: National Natural Science Foundation of China, Xidian University