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Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries.

Svenja Mehringer1, Enrico Seiler2, Felix Droop2

  • 1Department of Mathematics and Computer Science, Freie Universität Berlin, Takustr. 9, 14195, Berlin, Germany. svenja.mehringer@fu-berlin.de.

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|May 31, 2023
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Summary
This summary is machine-generated.

We developed a new Hierarchical Interleaved Bloom Filter (HIBF) for fast and space-efficient sequence searching in large databases. This novel data structure significantly outperforms existing tools in speed and memory usage while maintaining high accuracy.

Keywords:
Alignment free analysisApproximate membership queryBloom filterMetagenomicsMiminizerSequence search

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Area of Science:

  • Computer Science
  • Bioinformatics
  • Data Structures

Background:

  • Searching large sequence databases is computationally intensive.
  • Existing data structures often face trade-offs between speed, memory efficiency, and accuracy.

Purpose of the Study:

  • To introduce a novel, highly efficient data structure for sequence searching.
  • To demonstrate the performance advantages of the Hierarchical Interleaved Bloom Filter (HIBF) over state-of-the-art methods.

Main Methods:

  • Development of the Hierarchical Interleaved Bloom Filter (HIBF) data structure.
  • Comparative analysis of HIBF against existing tools on build time, index size, and search time.
  • Evaluation of accuracy for approximate membership queries.

Main Results:

  • HIBF demonstrates superior performance in build time (up to 211x faster), index size (up to 14x smaller), and search time (up to 129x faster).
  • Achieves comparable or better accuracy than current state-of-the-art tools.
  • HIBF is a general-purpose data structure applicable to various database searching applications.

Conclusions:

  • The Hierarchical Interleaved Bloom Filter (HIBF) offers significant improvements in efficiency for sequence searching.
  • HIBF provides a powerful and versatile engine for diverse data-intensive applications.
  • This novel data structure represents a substantial advancement in database searching technology.