ArticleGenome biology2009
Genomic DNA k-mer spectra: models and modalities.
Article in Genome biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 115 papers.
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Who cites it
115 citing papers in PubMed.
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- RNA-Lexis: a probabilistic algorithm using a non-parametric segmentation logic to detect meaningful sequences in RNA.Nucleic acids research · 2026Article
- Deciphering 6-mer Spectra Distribution Rules in Coronavirus Genomes: Application to Comparative Genomic Analysis.International journal of molecular sciences · 2026Article
- Sequence-Based Models for RNA-Protein Interactions Imputation Might Be Insufficient for Novel Signal Prediction in eCLIP Data.International journal of molecular sciences · 2026Article
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- Genome assembly and population genomic analysis reveal the genetic basis of popcorn evolution.Plant biotechnology journal · 2025Article
- Identifying associations of de novo noncoding variants with autism through integration of gene expression, sequence, and sex information.Genome biology · 2025Article
- MAFcounter: an efficient tool for counting the occurrences of k-mers in MAF files.BMC bioinformatics · 2025Article
- Genomic garden: From societal and scientific impacts to biodiversity conservation.Cell genomics · 2025Review
- GRAMEP: an alignment-free method based on the maximum entropy principle for identifying SNPs.BMC bioinformatics · 2025Article
- Identification of the shortest species-specific oligonucleotide sequences.Genome research · 2025Article
- A comparative study of antibiotic resistance patterns in Mycobacterium tuberculosis.Scientific reports · 2025Article
- Accurate assembly of full-length consensus for viral quasispecies.BMC bioinformatics · 2025Article
- CGSDA: inferring snoRNA-disease associations via ChebNetII and GatedGCN.Frontiers in genetics · 2025Article
- Investigating DNA words and their distributions across the tree of life.Computational and structural biotechnology journal · 2025Article
- EpiGePT: a pretrained transformer-based language model for context-specific human epigenomics.Genome biology · 2024Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
55 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe empirical frequencies of DNA k-mers in whole genome sequences provide an interesting perspective on genomic complexity, and the availability of large segments of genomic sequence from many organisms means that analysis of k-mers with non-trivial lengths is now possible.
resultsWe have studied the k-mer spectra of more than 100 species from Archea, Bacteria, and Eukaryota, particularly looking at the modalities of the distributions. As expected, most species have a unimodal k-mer spectrum. However, a few species, including all mammals, have multimodal spectra. These species coincide with the tetrapods. Genomic sequences are clearly very complex, and cannot be fully explained by any simple probabilistic model. Yet we sought such an explanation for the observed modalities, and discovered that low-order Markov models capture this property (and some others) fairly well.
conclusionsMultimodal spectra are characterized by specific ranges of values of C+G content and of CpG dinucleotide suppression, a range that encompasses all tetrapods analyzed. Other genomes, like that of the protozoa Entamoeba histolytica, which also exhibits CpG suppression, do not have multimodal k-mer spectra. Groupings of functional elements of the human genome also have a clear modality, and exhibit either a unimodal or multimodal behaviour, depending on the two above mentioned values.
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