ArticleBioinformatics (Oxford, England)2023
Block Aligner: an adaptive SIMD-accelerated aligner for sequences and position-specific scoring matrices.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed.
- Efficient sequence alignment against millions of prokaryotic genomes with LexicMap.Nature biotechnology · 2026Article
- Accelign: a GPU-based library for accelerating pairwise sequence alignment.BMC bioinformatics · 2026Article
- Sassy: fuzzy searching DNA sequences using SIMD.Bioinformatics (Oxford, England) · 2026Article
- High-resolution metagenome assembly for modern long reads with myloasm.Nature biotechnology · 2026Article
- An efficient framework for protein-protein interaction prediction by integrating stacked denoising autoencoders and random ferns.iScience · 2026Article
- Long-read reconstruction of many diverse haplotypes with devider.Genome research · 2025Article
- High-resolution metagenome assembly for modern long reads with myloasm.bioRxiv : the preprint server for biology · 2025Article
- Predicting protein-protein interactions in microbes associated with cardiovascular diseases using deep denoising autoencoders and evolutionary information.Frontiers in pharmacology · 2025Article
- FORAlign: accelerating gap-affine DNA pairwise sequence alignment using FOR-blocks based on Four Russians approach with linear space complexity.Briefings in bioinformatics · 2024Article
- An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models.BMC bioinformatics · 2024Article
- Exact global alignment using A* with chaining seed heuristic and match pruning.Bioinformatics (Oxford, England) · 2024Article
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2 authors.
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Abstract
motivationEfficiently aligning sequences is a fundamental problem in bioinformatics. Many recent algorithms for computing alignments through Smith-Waterman-Gotoh dynamic programming (DP) exploit Single Instruction Multiple Data (SIMD) operations on modern CPUs for speed. However, these advances have largely ignored difficulties associated with efficiently handling complex scoring matrices or large gaps (insertions or deletions).
resultsWe propose a new SIMD-accelerated algorithm called Block Aligner for aligning nucleotide and protein sequences against other sequences or position-specific scoring matrices. We introduce a new paradigm that uses blocks in the DP matrix that greedily shift, grow, and shrink. This approach allows regions of the DP matrix to be adaptively computed. Our algorithm reaches over 5-10 times faster than some previous methods while incurring an error rate of less than 3% on protein and long read datasets, despite large gaps and low sequence identities. AVAILABILITY AND IMPLEMENTATION: Our algorithm is implemented for global, local, and X-drop alignments. It is available as a Rust library (with C bindings) at https://github.com/Daniel-Liu-c0deb0t/block-aligner.
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