Dynamic partitioning of search patterns for approximate pattern matching using search schemes

Renders, Luca; Marchal, Kathleen; Fostier, Jan

doi:10.1016/j.isci.2021.102687

Cited by 6 publications

(4 citation statements)

References 15 publications

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“…This means we report all occurrences within a pre-specified Hamming or edit distance. This functionality is similar to that provided by lossless read-mapper Columba (developed in the same research group) [25, 23, 24], but Columba’s index is based on the bidirectional FM-index ( O ( n ) memory requirements). To ensure practical efficiency in b-move, we incorporated several optimizations originally developed for Columba: optimized edit distance to reduce redundancy, superior search schemes replacing pigeonhole methods, a lookup-table to bypass matching the first 10-mers, dynamic pattern partitioning, and bit-parallel pattern matching.…”

Section: Resultsmentioning

confidence: 99%

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b-move: faster bidirectional character extensions in a run-length compressed index

Depuydt,

Renders,

Van de Vyver

et al. 2024

Preprint

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Due 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. We introduce b-move, a novel bidirectional extension of the move structure, enabling fast, cache-efficient bidirectional character extensions in run-length compressed space. It achieves bidirectional character extensions up to 8 times faster than the br-index, closing the performance gap with FM-index-based alternatives, while maintaining the br-index’s favorable memory characteristics. For example, all available completeE. coligenomes on NCBI’s RefSeq collection can be compiled into a b-move index that fits into the RAM of a typical laptop. Thus, b-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 athttps://github.com/biointec/b-moveunder the AGPL-3.0 license.FundingLore Depuydt: PhD Fellowship FR (1117322N), Research Foundation – Flanders (FWO)Luca Renders: PhD Fellowship SB (1SE7822N), Research Foundation – Flanders (FWO)Travis Gagie: NSERC Discovery Grant RGPIN-07185-2020 to Travis Gagie and NIH grant R01HG011392 to Ben Langmead

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Section: Resultsmentioning

confidence: 99%

“…For example, approximate matches of a pattern can be sought using the pigeonhole principle or, more generally, search schemes [16]. The demonstrated efficiency of search schemes, for example in lossless read-mapper Columba [25, 23, 24], motivates the need for fast bidirectional character extensions.…”

Section: Preliminariesmentioning

confidence: 99%

b-move: faster bidirectional character extensions in a run-length compressed index

Depuydt,

Renders,

Van de Vyver

et al. 2024

Preprint

Self Cite

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“…Briefly, search schemes are a new class of sequence alignment algorithms that define how a pattern is matched using a bidirectional full-text index such that unsuccessful branches are discarded as quickly as possible, and runtime is minimized. Their excellent performance has been demonstrated for linear reference genomes [35,36,37,38]. In contrast to lossy heuristics (that often rely on the seed-and-extend paradigm), search schemes are lossless: they guarantee to retrieve all occurrences within a pre-specified number of errors.…”

Section: Contributionsmentioning

confidence: 99%

“…The construction process of the underlying bidirectional FM-index is based on the implementation of Columba [38,41]. The construction of components G and B is similar to the algorithms described in [31].…”

Section: Building the Data Structurementioning

confidence: 99%

Pan-genome de Bruijn Graph using the Bidirectional FM-index

Depuydt

Renders

Abeel

et al. 2023

Preprint

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Background: Pan-genome graphs are gaining importance in the field of bioinformatics as data structures to represent and jointly analyze multiple genomes. Compacted de Bruijn graphs are inherently suited for this purpose, as their graph topology naturally reveals similarity and divergence within the pan-genome. Most state-of-the-art pan-genome graphs are represented explicitly in terms of nodes and edges. Recently, an alternative, implicit graph representation was proposed that builds directly upon the unidirectional FM-index. As such, a memory-efficient graph data structure is obtained that inherits the FM-index' backward search functionality. However, this representation suffers from a number of shortcomings in terms of functionality and algorithmic performance. Results: We present a data structure for a pan-genome, compacted de Bruijn graph that aims to address these shortcomings. It is built on the bidirectional FM-index, extending the ability of its unidirectional counterpart to navigate and search the graph in both directions. All basic graph navigation steps can be performed in constant time. Based on these features, we implement subgraph visualization as well as lossless read-to-graph alignment using search schemes. We demonstrate that we can retrieve all occurrences corresponding to a read within a certain edit distance in a very efficient manner. Through a case study, we show the potential of exploiting the information embedded in the graph's topology through visualization and sequence alignment. Conclusions: We propose a memory-efficient representation of the pan-genome graph that supports subgraph visualization and lossless alignment of reads against the graph using search schemes. The C++ source code of our software, called Nexus, is available at https://github.com/biointec/nexus under AGPL-3.0 license.

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Automated Design of Efficient Search Schemes for Lossless Approximate Pattern Matching

Renders,

Depuydt,

Rahmann

et al. 2024

Lecture Notes in Computer Science

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Dynamic partitioning of search patterns for approximate pattern matching using search schemes

Cited by 6 publications

References 15 publications

b-move: faster bidirectional character extensions in a run-length compressed index

b-move: faster bidirectional character extensions in a run-length compressed index

Pan-genome de Bruijn Graph using the Bidirectional FM-index

Automated Design of Efficient Search Schemes for Lossless Approximate Pattern Matching

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