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  Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries

Mehringer, S., Seiler, E., Droop, F., Mitra, D., Rahn, R., Vingron, M., et al. (2023). Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries. Genome Biology: Biology for the Post-Genomic Era, 24(1): 131. doi:10.1186/s13059-023-02971-4.

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Item Permalink: https://hdl.handle.net/21.11116/0000-000D-C564-4 Version Permalink: https://hdl.handle.net/21.11116/0000-000E-558D-4
Genre: Journal Article

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GenomeBiol_Mehringer et al_2023.pdf (Publisher version), 3MB
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© The Author(s) 2023
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 Creators:
Mehringer, Svenja1, Author                 
Seiler, Enrico1, Author                 
Droop, Felix 2, Author
Mitra, Darvish1, Author           
Rahn, René1, Author           
Vingron, Martin3, Author                 
Reinert, Knut4, Author                 
Affiliations:
1IMPRS for Biology and Computation (Anne-Dominique Gindrat), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479666              
2Department of Mathematics and Computer Science, Freie Universität Berlin, Takustr. 9, 14195 Berlin, Germany, ou_persistent22              
3Transcriptional Regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              
4Efficient Algorithms for Omics Data (Knut Reinert), Max Planck Fellow Group, Max Planck Institute for Molecular Genetics, Max Planck Society, ou_2385698              

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 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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Language(s): eng - English
 Dates: 2023-05-112023-05-31
 Publication Status: Published online
 Pages: -
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 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1186/s13059-023-02971-4
PMID: 37259161
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Title: Genome Biology : Biology for the Post-Genomic Era
  Other : Genome Biology
Source Genre: Journal
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Publ. Info: London : BioMed Central Ltd.
Pages: - Volume / Issue: 24 (1) Sequence Number: 131 Start / End Page: - Identifier: ISSN: 1474-760X
ISSN: 1465-6906
CoNE: https://pure.mpg.de/cone/journals/resource/1000000000224390