ArticleGenome research2023
Aligning distant sequences to graphs using long seed sketches.
Article in Genome research, 2023. 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.
- Multi-context seeds enable fast and high-accuracy read mapping.Genome biology · 2026Article
- MELO-ED: learning locality-sensitive multi-embeddings for edit distance.bioRxiv : the preprint server for biology · 2025Article
- Edit Distance Embedding with Genomic Large Language Model.bioRxiv : the preprint server for biology · 2025Article
- A survey of sequence-to-graph mapping algorithms in the pangenome era.Genome biology · 2025Review
- Label-guided seed-chain-extend alignment on annotated De Bruijn graphs.Bioinformatics (Oxford, England) · 2024Article
- A survey of mapping algorithms in the long-reads era.Genome biology · 2023Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sequence-to-graph alignment is crucial for applications such as variant genotyping, read error correction, and genome assembly. We propose a novel seeding approach that relies on long inexact matches rather than short exact matches, and show that it yields a better time-accuracy trade-off in settings with up to a [Formula: see text] mutation rate. We use sketches of a subset of graph nodes, which are more robust to indels, and store them in a k-nearest neighbor index to avoid the curse of dimensionality. Our approach contrasts with existing methods and highlights the important role that sketching into vector space can play in bioinformatics applications. We show that our method scales to graphs with 1 billion nodes and has quasi-logarithmic query time for queries with an edit distance of [Formula: see text] For such queries, longer sketch-based seeds yield a [Formula: see text] increase in recall compared with exact seeds. Our approach can be incorporated into other aligners, providing a novel direction for sequence-to-graph alignment.
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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.