ArticleBriefings in bioinformatics2024
FORAlign: accelerating gap-affine DNA pairwise sequence alignment using FOR-blocks based on Four Russians approach with linear space complexity.
Article in Briefings in bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
3 citing papers in PubMed.
- Singletrack: an algorithm for improving memory consumption and performance of gap-affine sequence alignment.Bioinformatics (Oxford, England) · 2026Article
- Advancing single-cell omics and cell-based therapeutics with quantum computing.Nature reviews. Molecular cell biology · 2026Review
- deMEM: a novel divide-and-conquer framework based on de Bruijn graph for scalable multiple sequence alignment.GigaScience · 2026Article
Corrections and comments
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Authors and funding
5 authors.
Funding
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.
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Registered trials
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