ArticleiScience2024
Movi: A fast and cache-efficient full-text pangenome index.
Article in iScience, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Movi 2: fast and space-efficient queries on pangenomes.Bioinformatics (Oxford, England) · 2026Article
- RLBWT-based LCP computation in compressed space for terabase-scale pangenome analysis.Bioinformatics (Oxford, England) · 2026Article
- Building genomic data structures from compressed representations using prefix-free parsing.Genome research · 2026Review
- Minimizing reference bias with an imputed personalized reference.Genome research · 2026Article
- Antibiotic Exposure Through Human Milk Influences the Infant Gut Microbiome.bioRxiv : the preprint server for biology · 2026Article
- Household environmental characteristics influence the house dust metagenome.Environmental research · 2026Article
- RLBWT-Based LCP Computation in Compressed Space for Terabase-Scale Pangenome Analysis.bioRxiv : the preprint server for biology · 2026Article
- Bounding the Average Move Structure Query for Faster and Smaller RLBWT Permutations.LIPIcs : Leibniz international proceedings in informatics · 2026Article
- Col-BWT: Pangenomic Seed Chaining with Maximal Matches Improves Read Classification.Journal of computational biology : a journal of computational molecular cell biology · 2026Article
- Article
- Environmental and maternal imprints on infant gut metabolic development.Cell host & microbe · 2025Article
- Robust 16S rRNA classification based on a compressed LCA index.Genome research · 2025Article
- Columba: fast approximate pattern matching with optimized search schemes.Bioinformatics (Oxford, England) · 2025Article
- Movi 2: Fast and Space-Efficient Queries on Pangenomes.bioRxiv : the preprint server for biology · 2025Article
- Abundance ofmSphere · 2025Article
- Versatile wastewater monitoring of pathogens and antimicrobial resistance enabled by metatranscriptomics and long-read metagenomics.Research square · 2025Article
- b-move: faster lossless approximate pattern matching in a run-length compressed index.Algorithms for molecular biology : AMB · 2025Article
- Environmental and Maternal Imprints on Infant Gut Metabolic Programming.bioRxiv : the preprint server for biology · 2025Article
- Mumemto: efficient maximal matching across pangenomes.Genome biology · 2025Article
- Efficient and robust search of microbial genomes via phylogenetic compression.Nature methods · 2025Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Pangenome indexes are promising tools for many applications, including classification of nanopore sequencing reads. Move structure is a compressed-index data structure based on the Burrows-Wheeler Transform (BWT). It offers simultaneous O(1)-time queries and O(r) space, where r is the number of BWT runs (consecutive sequence of identical characters). We developed Movi based on the move structure for indexing and querying pangenomes. Movi scales very well for repetitive text as its size grows strictly by r. Movi computes sophisticated matching queries for classification such as pseudo-matching lengths and backward search up to 30 times faster than existing methods by minimizing the number of cache misses and using memory prefetching to attain a degree of latency hiding. Movi's fast constant-time query loop makes it well suited to real-time applications like adaptive sampling for nanopore sequencing, where decisions must be made in a small and predictable time interval.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.