ArticlePloS one2021
Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy.
Article in PloS one, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Efficient and interpretable DNA/RNA representation using Komlós-Hadamard transforms.BMC bioinformatics · 2026Article
- StaLAENet: A stacked LSTM-nested deep-autoencoder network for identification of antimicrobial resistance of nosocomial pathogens.Journal of biosciences · 2026Article
- Flow Cytometry and K-mer-Based Approach for Genome Size Estimation of Clusterbean: A Case Study.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Elucidating Transitions ofJournal of computational biology : a journal of computational molecular cell biology · 2026Article
- Multidimensional Gene Space as an Approach for Analyzing the Organization of Genomes.International journal of molecular sciences · 2025Article
- Machine Learning Enables Alignment-Free Distance Calculation and Phylogenetic Placement Using k-Mer Frequencies.Molecular ecology resources · 2025Article
- Organism-Specific Sequence Motifs Link Ribosomal RNAs to Brain Disorders.Molecular biology and evolution · 2025Article
- Energy entropy vector: a novel approach for efficient microbial genomic sequence analysis and classification.Briefings in bioinformatics · 2025Article
- Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes.mSystems · 2025Article
- Prokrustean Graph: A substring index for rapid k-mer size analysis.bioRxiv : the preprint server for biology · 2025Article
- EvANI benchmarking workflow for evolutionary distance estimation.Briefings in bioinformatics · 2025Article
- bpRNA-CosMoS: a robust and efficient RNA structural comparison method using k-mer based cosine similarity.Bioinformatics (Oxford, England) · 2025Article
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- Rapid, reference-free identification of bacterial pathogen transmission using optimized splitMicrobial genomics · 2025Article
- EvANI benchmarking workflow for evolutionary distance estimation.bioRxiv : the preprint server for biology · 2025Article
- Identification of the shortest species-specific oligonucleotide sequences.Genome research · 2025Article
- MDFGNN-SMMA: prediction of potential small molecule-miRNA associations based on multi-source data fusion and graph neural networks.BMC bioinformatics · 2025Article
- Essential nucleic acid omics: a theoretical foundation for early-stage users.Frontiers in bioinformatics · 2025Review
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- Article
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Authors and funding
3 authors.
Funding
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Abstract
Information theoretic approaches are ubiquitous and effective in a wide variety of bioinformatics applications. In comparative genomics, alignment-free methods, based on short DNA words, or k-mers, are particularly powerful. We evaluated the utility of varying k-mer lengths for genome comparisons by analyzing their sequence space coverage of 5805 genomes in the KEGG GENOME database. In subsequent analyses on four k-mer lengths spanning the relevant range (11, 21, 31, 41), hierarchical clustering of 1634 genus-level representative genomes using pairwise 21- and 31-mer Jaccard similarities best recapitulated a phylogenetic/taxonomic tree of life with clear boundaries for superkingdom domains and high subtree similarity for named taxons at lower levels (family through phylum). By analyzing ~14.2M prokaryotic genome comparisons by their lowest-common-ancestor taxon levels, we detected many potential misclassification errors in a curated database, further demonstrating the need for wide-scale adoption of quantitative taxonomic classifications based on whole-genome similarity.
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