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b-move: Faster Lossless Approximate Pattern Matching in a Run-Length Compressed Index.

Lore Depuydt1, Luca Renders1, Simon Van de Vyver2

  • 1Ghent University - imec, Technologiepark 126, 9052 Ghent, Belgium.

Research Square
|November 28, 2024
PubMed
Summary
This summary is machine-generated.

The new b-move index offers fast and memory-efficient approximate pattern matching for large pan-genome datasets, outperforming previous methods. This bioinformatics tool is practical for diverse genome analysis, fitting even on standard laptops.

Keywords:
Approximate Pattern MatchingBidirectional SearchCache EfficiencyFM-indexLossless AlignmentMove StructurePan-genomicsr-index

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Pan-genomes are increasingly used over reference genomes to capture genetic diversity.
  • Traditional FM-index tools struggle with memory limitations for large genome collections.
  • Existing compressed indices like r-index and move structure have limitations in bidirectional search or incur high computational overhead.

Purpose of the Study:

  • To introduce b-move, a novel extension of the move structure for efficient approximate pattern matching in compressed sequence data.
  • To address the memory and computational challenges posed by large pan-genome datasets in bioinformatics.

Main Methods:

  • Development of b-move, a bidirectional extension of the move structure.
  • Implementation of lossless approximate pattern matching and locate functionality.
  • Utilizing run-length compressed space for index construction.

Main Results:

  • b-move achieves fast, cache-efficient, and lossless approximate pattern matching.
  • Bidirectional character extensions are up to 7 times faster than the br-index.
  • The b-move index for complete E. coli genomes fits within typical laptop RAM, demonstrating memory efficiency.

Conclusions:

  • b-move is a practical and scalable solution for pan-genome indexing and querying.
  • The C++ implementation of b-move supports efficient pattern matching and locate functionality.
  • The tool is publicly available for use in bioinformatics research.