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

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 a...

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Vydáno v:Briefings in bioinformatics Ročník 26; číslo 1
Hlavní autoři: Wei, Yanming, Zhou, Tong, Zhai, Yixiao, Yu, Liang, Zou, Quan
Médium: Journal Article
Jazyk:angličtina
Vydáno: England Oxford University Press 22.11.2024
Témata:
Algorithms
Computational Biology - methods
Humans
Problem Solving Protocol
Sequence Alignment - methods
Sequence Analysis, DNA - methods
Software
parallel algorithm design
dynamic programming
four Russians speedup
sequence alignment
ISSN:1467-5463, 1477-4054, 1477-4054
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Shrnutí: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.
Bibliografie:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
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These authors (LY and ZQ) should be considered as co-corresponding authors.
ISSN:1467-5463
1477-4054
1477-4054
DOI:10.1093/bib/bbaf061