ArticleNAR genomics and bioinformatics2023
BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis.
Article in NAR genomics and bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Hash functions in nucleotide sequence analysis.Genome research · 2026Review
- Multi-context seeds enable fast and high-accuracy read mapping.Genome biology · 2026Article
- Rawsamble: overlapping raw nanopore signals using a hash-based seeding mechanism.Bioinformatics (Oxford, England) · 2026Article
- FEDRANN: effective long-read overlap detection based on dimensionality reduction and approximate nearest neighbors.GigaScience · 2026Article
- wholeskim: Utilising Genome Skims for Taxonomically Annotating Ancient DNA Metagenomes.Molecular ecology resources · 2025Article
- Taming large-scale genomic analyses via sparsified genomics.Nature communications · 2025Article
- xRead: a coverage-guided approach for scalable construction of read overlapping graph.GigaScience · 2025Article
- Advancing microbial diagnostics: a universal phylogeny guided computational algorithm to find unique sequences for precise microorganism detection.Briefings in bioinformatics · 2024Article
- Improved sub-genomic RNA prediction with the ARTIC protocol.Nucleic acids research · 2024Article
- Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome.Nucleic acids research · 2024Article
- RawHash2: mapping raw nanopore signals using hash-based seeding and adaptive quantization.Bioinformatics (Oxford, England) · 2024Article
- Designing efficient randstrobes for sequence similarity analyses.Bioinformatics (Oxford, England) · 2024Article
- TargetCall: eliminating the wasted computation in basecalling via pre-basecalling filtering.Frontiers in genetics · 2024Article
- dna2bit: high performance genomic distance estimation software for microbial genome analysis.Frontiers in microbiology · 2024Article
- LexicHash: sequence similarity estimation via lexicographic comparison of hashes.Bioinformatics (Oxford, England) · 2023Article
- Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation.Bioinformatics (Oxford, England) · 2023Article
- Efficient mapping of accurate long reads in minimizer space with mapquik.Genome research · 2023Article
- Entropy predicts sensitivity of pseudorandom seeds.Genome research · 2023Article
- RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes.Bioinformatics (Oxford, England) · 2023Article
- A survey of mapping algorithms in the long-reads era.Genome biology · 2023Review
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Generating the hash values of short subsequences, called seeds, enables quickly identifying similarities between genomic sequences by matching seeds with a single lookup of their hash values. However, these hash values can be used only for finding exact-matching seeds as the conventional hashing methods assign distinct hash values for different seeds, including highly similar seeds. Finding only exact-matching seeds causes either (i) increasing the use of the costly sequence alignment or (ii) limited sensitivity. We introduce
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