ArticleJournal of computational biology : a journal of computational molecular cell biology2021
Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- 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
- Sketching Methods with Small Window Guarantee Using Minimum Decycling Sets.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
- Efficient minimizer orders for large values ofGenome research · 2023Article
- Theory of local k-mer selection with applications to long-read alignment.Bioinformatics (Oxford, England) · 2022Article
- Space-efficient representation of genomic k-mer count tables.Algorithms for molecular biology : AMB · 2022Article
- Improved design and analysis of practical minimizers.Bioinformatics (Oxford, England) · 2020Article
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Authors and funding
3 authors.
Funding
Abstract
Universal hitting sets (UHS) are sets of words that are unavoidable: every long enough sequence is hit by the set (i.e., it contains a word from the set). There is a tight relationship between UHS and minimizer schemes, where minimizer schemes with low density (i.e., efficient schemes) correspond to UHS of small size. Local schemes are a generalization of minimizer schemes that can be used as replacement for minimizer scheme with the possibility of being much more efficient. We establish the link between efficient local schemes and the minimum length of a string that must be hit by a UHS. We give bounds for the remaining path length of the Mykkeltveit UHS. In addition, we create a local scheme with the lowest known density that is only a log factor away from the theoretical lower bound.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.