ArticleAlgorithms for molecular biology : AMB2025
b-move: faster lossless approximate pattern matching in a run-length compressed index.
Article in Algorithms for molecular biology : AMB, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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2 citing papers in PubMed.
- KeBaB:International Symposium on String Processing and Information Retrieval : SPIRE ... : proceedings. SPIRE (Symposium) · 2026Article
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6 authors.
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Abstract
backgroundDue to the increasing availability of high-quality genome sequences, pan-genomes are gradually replacing single consensus reference genomes in many bioinformatics pipelines to better capture genetic diversity. Traditional bioinformatics tools using the FM-index face memory limitations with such large genome collections. Recent advancements in run-length compressed indices like Gagie et al.'s r-index and Nishimoto and Tabei's move structure, alleviate memory constraints but focus primarily on backward search for MEM-finding. Arakawa et al.'s br-index initiates complete approximate pattern matching using bidirectional search in run-length compressed space, but with significant computational overhead due to complex memory access patterns.
resultsWe introduce b-move, a novel bidirectional extension of the move structure, enabling fast, cache-efficient, lossless approximate pattern matching in run-length compressed space. It achieves bidirectional character extensions up to 7 times faster than the br-index, closing the performance gap with FM-index-based alternatives. For locating occurrences, b-move performs
conclusionsb-move proves practical and scalable for pan-genome indexing and querying. We provide a C++ implementation of b-move, supporting efficient lossless approximate pattern matching including locate functionality, available at https://github.com/biointec/b-move under the AGPL-3.0 license.
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