ArticleNature biotechnology2026
Efficient sequence alignment against millions of prokaryotic genomes with LexicMap.
Article in Nature biotechnology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics.bioRxiv : the preprint server for biology · 2026Article
- Novel transposon TnMicrobial genomics · 2026Article
- Effects of Dominant Fungi on Wheat Quality During Storage.Foods (Basel, Switzerland) · 2026Article
- Artificial Intelligence for Microbial Isolation and Cultivation: Progress and Challenges.Microorganisms · 2026Review
- Novel transposon TnmedRxiv : the preprint server for health sciences · 2026Article
- Multi-context seeds enable fast and high-accuracy read mapping.Genome biology · 2026Article
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Authors and funding
3 authors.
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Abstract
The size of microbial sequence databases continues to grow beyond the abilities of existing alignment tools. We introduce LexicMap, a nucleotide sequence alignment tool for efficiently querying moderate-length sequences (>250 bp) such as a gene, plasmid or long read against up to millions of prokaryotic genomes. We construct a small set of probe k-mers, which are selected to efficiently sample the entire database to be indexed such that every 250-bp window of each database genome contains multiple seed k-mers, each with a shared prefix with one of the probes. Storing these seeds in a hierarchical index enables fast and low-memory alignment. We benchmark both accuracy and potential to scale to databases of millions of bacterial genomes, showing that LexicMap achieves comparable accuracy to state-of-the-art methods but with greater speed and lower memory use. Our method supports querying at scale and within minutes, which will be useful for many biological applications across epidemiology, ecology and evolution.
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