ArticleBioinformatics (Oxford, England)2018
Asymptotically optimal minimizers schemes.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Min-frame transformation enables more sensitive viral genome alignment.bioRxiv : the preprint server for biology · 2026Article
- Multi-context seeds enable fast and high-accuracy read mapping.Genome biology · 2026Article
- Density-reducing Jaccard estimators for sketch-based long read applications.BMC bioinformatics · 2025Article
- MELO-ED: learning locality-sensitive multi-embeddings for edit distance.bioRxiv : the preprint server for biology · 2025Article
- Efficient seeding for error-prone sequences with SubseqHash2.Bioinformatics (Oxford, England) · 2025Article
- GreedyMini: generating low-density DNA minimizers.Bioinformatics (Oxford, England) · 2025Article
- Sequence similarity estimation by random subsequence sketching.bioRxiv : the preprint server for biology · 2025Article
- The open-closed mod-minimizer algorithm.Algorithms for molecular biology : AMB · 2025Article
- A near-tight lower bound on the density of forward sampling schemes.Bioinformatics (Oxford, England) · 2024Article
- A near-tight lower bound on the density of forward sampling schemes.bioRxiv : the preprint server for biology · 2024Article
- k-nonical space: sketching with reverse complements.Bioinformatics (Oxford, England) · 2024Article
- When less is more: sketching with minimizers in genomics.Genome biology · 2024Review
- Sketching Methods with Small Window Guarantee Using Minimum Decycling Sets.Journal of computational biology : a journal of computational molecular cell biology · 2024Article
- Density and Conservation Optimization of the Generalized Masked-Minimizer Sketching Scheme.Journal of computational biology : a journal of computational molecular cell biology · 2024Article
- OCTOPUS: Disk-based, Multiplatform, Mobile-friendly Metagenomics Classifier.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2024Article
- Creating and Using Minimizer Sketches in Computational Genomics.Journal of computational biology : a journal of computational molecular cell biology · 2023Review
- Article
- LexicHash: sequence similarity estimation via lexicographic comparison of hashes.Bioinformatics (Oxford, England) · 2023Article
- ViralVectors: compact and scalable alignment-free virome feature generation.Medical & biological engineering & computing · 2023Article
- Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation.Bioinformatics (Oxford, England) · 2023Article
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3 authors.
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Abstract
Motivation: The minimizers technique is a method to sample k-mers that is used in many bioinformatics software to reduce computation, memory usage and run time. The number of applications using minimizers keeps on growing steadily. Despite its many uses, the theoretical understanding of minimizers is still very limited. In many applications, selecting as few k-mers as possible (i.e. having a low density) is beneficial. The density is highly dependent on the choice of the order on the k-mers. Different applications use different orders, but none of these orders are optimal. A better understanding of minimizers schemes, and the related local and forward schemes, will allow designing schemes with lower density and thereby making existing and future bioinformatics tools even more efficient. Results: From the analysis of the asymptotic behavior of minimizers, forward and local schemes, we show that the previously believed lower bound on minimizers schemes does not hold, and that schemes with density lower than thought possible actually exist. The proof is constructive and leads to an efficient algorithm to compare k-mers. These orders are the first known orders that are asymptotically optimal. Additionally, we give improved bounds on the density achievable by the three type of schemes.
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