ArticleGenome biology2023
Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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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
8 citing papers in PubMed.
- Kaminari: a frugal colored index for approximateBioinformatics advances · 2026Article
- Article
- ganon2: up-to-date and scalable metagenomics analysis.NAR genomics and bioinformatics · 2025Article
- TetRex: a novel algorithm for index-accelerated search of highly conserved motifs.NAR genomics and bioinformatics · 2025Article
- Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters.Genome research · 2024Article
- Indexing and searching petabase-scale nucleotide resources.Nature methods · 2024Article
- A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline.Genome biology · 2024Article
- Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA.Nature computational science · 2024Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a novel data structure for searching sequences in large databases: the Hierarchical Interleaved Bloom Filter (HIBF). It is extremely fast and space efficient, yet so general that it could serve as the underlying engine for many applications. We show that the HIBF is superior in build time, index size, and search time while achieving a comparable or better accuracy compared to other state-of-the-art tools. The HIBF builds an index up to 211 times faster, using up to 14 times less space, and can answer approximate membership queries faster by a factor of up to 129.
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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.