ArticleAlgorithms for molecular biology : AMB2021
An optimized FM-index library for nucleotide and amino acid search.
Article in Algorithms for molecular biology : AMB, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed.
- Engineering rank queries on bit vectors and strings.Algorithms for molecular biology : AMB · 2025Article
- Movi: A fast and cache-efficient full-text pangenome index.iScience · 2024Article
- SigAlign: an alignment algorithm guided by explicit similarity criteria.Nucleic acids research · 2024Article
- nail: software for high-speed, high-sensitivity protein sequence annotation.bioRxiv : the preprint server for biology · 2024Article
- From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures.Computational and structural biotechnology journal · 2022Review
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2 authors.
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Abstract
backgroundPattern matching is a key step in a variety of biological sequence analysis pipelines. The FM-index is a compressed data structure for pattern matching, with search run time that is independent of the length of the database text. Implementation of the FM-index is reasonably complicated, so that increased adoption will be aided by the availability of a fast and flexible FM-index library.
resultsWe present AvxWindowedFMindex (AWFM-index), a lightweight, open-source, thread-parallel FM-index library written in C that is optimized for indexing nucleotide and amino acid sequences. AWFM-index introduces a new approach to storing FM-index data in a strided bit-vector format that enables extremely efficient computation of the FM-index occurrence function via AVX2 bitwise instructions, and combines this with optional on-disk storage of the index's suffix array and a cache-efficient lookup table for partial k-mer searches. The AWFM-index performs exact match count and locate queries faster than SeqAn3's FM-index implementation across a range of comparable memory footprints. When optimized for speed, AWFM-index is [Formula: see text]2-4x faster than SeqAn3 for nucleotide search, and [Formula: see text]2-6x faster for amino acid search; it is also [Formula: see text]4x faster with similar memory footprint when storing the suffix array in on-disk SSD storage.
conclusionsAWFM-index is easy to incorporate into bioinformatics software, offers run-time performance parameterization, and provides clients with FM-index functionality at both a high-level (count or locate all instances of a query string) and low-level (step-wise control of the FM-index backward-search process). The open-source library is available for download at https://github.com/TravisWheelerLab/AvxWindowFmIndex.
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