ArticleBioinformatics (Oxford, England)2021
Sequence-specific minimizers via polar sets.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed.
- GreedyMini: generating low-density DNA minimizers.Bioinformatics (Oxford, England) · 2025Article
- A near-tight lower bound on the density of forward sampling schemes.Bioinformatics (Oxford, England) · 2024Article
- The Statistics of Parametrized Syncmers in a Simple Mutation Process Without Spurious Matches.Journal of computational biology : a journal of computational molecular cell biology · 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
- A simple refined DNA minimizer operator enables 2-fold faster computation.Bioinformatics (Oxford, England) · 2024Article
- Density and Conservation Optimization of the Generalized Masked-Minimizer Sketching Scheme.Journal of computational biology : a journal of computational molecular cell biology · 2024Article
- Creating and Using Minimizer Sketches in Computational Genomics.Journal of computational biology : a journal of computational molecular cell biology · 2023Review
- Article
- Proving sequence aligners can guarantee accuracy in almostGenome research · 2023Article
- Entropy predicts sensitivity of pseudorandom seeds.Genome research · 2023Article
- Efficient minimizer orders for large values ofGenome research · 2023Article
- Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries.Genome biology · 2023Article
- How to optimally sample a sequence for rapid analysis.Bioinformatics (Oxford, England) · 2023Article
- Differentiable Learning of Sequence-Specific Minimizer Schemes with DeepMinimizer.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- Theory of local k-mer selection with applications to long-read alignment.Bioinformatics (Oxford, England) · 2022Article
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3 authors.
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Abstract
motivationMinimizers are efficient methods to sample k-mers from genomic sequences that unconditionally preserve sufficiently long matches between sequences. Well-established methods to construct efficient minimizers focus on sampling fewer k-mers on a random sequence and use universal hitting sets (sets of k-mers that appear frequently enough) to upper bound the sketch size. In contrast, the problem of sequence-specific minimizers, which is to construct efficient minimizers to sample fewer k-mers on a specific sequence such as the reference genome, is less studied. Currently, the theoretical understanding of this problem is lacking, and existing methods do not specialize well to sketch specific sequences.
resultsWe propose the concept of polar sets, complementary to the existing idea of universal hitting sets. Polar sets are k-mer sets that are spread out enough on the reference, and provably specialize well to specific sequences. Link energy measures how well spread out a polar set is, and with it, the sketch size can be bounded from above and below in a theoretically sound way. This allows for direct optimization of sketch size. We propose efficient heuristics to construct polar sets, and via experiments on the human reference genome, show their practical superiority in designing efficient sequence-specific minimizers. AVAILABILITY AND IMPLEMENTATION: A reference implementation and code for analyses under an open-source license are at https://github.com/kingsford-group/polarset. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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