ArticleBMC evolutionary biology2020
Intrinsic laws of k-mer spectra of genome sequences and evolution mechanism of genomes.
Article in BMC evolutionary biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Deciphering 6-mer Spectra Distribution Rules in Coronavirus Genomes: Application to Comparative Genomic Analysis.International journal of molecular sciences · 2026Article
- Regions Enriched with Reverse Complement Triplets in Bacterial Genomes.International journal of molecular sciences · 2026Article
- Genomic evolution of SARS-CoV-2 delta variants pre- and post-omicron emergence using alignment-free machine learning models.PloS one · 2026Article
- Elucidating Transitions ofJournal of computational biology : a journal of computational molecular cell biology · 2026Article
- Article
- CG-Based Stratification of 8-mers Highlights Functional Roles and Phylogenetic Divergence Markers.International journal of molecular sciences · 2025Article
- Exploring the Causes of the Cambrian Explosion Based on the Evolution Mechanism of Genome Sequences.Biology · 2025Article
- Prokrustean Graph: A substring index for rapid k-mer size analysis.bioRxiv : the preprint server for biology · 2025Article
- Difference Analysis Among Six Kinds of Acceptor Splicing Sequences by the Dispersion Features of 6-mer Subsets in Human Genes.Biology · 2025Article
- Investigating DNA words and their distributions across the tree of life.Computational and structural biotechnology journal · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- Distribution rules of 8-mer spectra and characterization of evolution state in animal genome sequences.BMC genomics · 2024Article
- The determinants of the rarity of nucleic and peptide short sequences in nature.NAR genomics and bioinformatics · 2024Article
- Frequentmers - a novel way to look at metagenomic next generation sequencing data and an application in detecting liver cirrhosis.BMC genomics · 2023Article
- Exploring objective feature sets in constructing the evolution relationship of animal genome sequences.BMC genomics · 2023Article
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8 authors.
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Abstract
backgroundK-mer spectra of DNA sequences contain important information about sequence composition and sequence evolution. We want to reveal the evolution rules of genome sequences by studying the k-mer spectra of genome sequences.
resultsThe intrinsic laws of k-mer spectra of 920 genome sequences from primate to prokaryote were analyzed. We found that there are two types of evolution selection modes in genome sequences, named as CG Independent Selection and TA Independent Selection. There is a mutual inhibition relationship between CG and TA independent selections. We found that the intensity of CG and TA independent selections correlates closely with genome evolution and G + C content of genome sequences. The living habits of species are related closely to the independent selection modes adopted by species genomes. Consequently, we proposed an evolution mechanism of genomes in which the genome evolution is determined by the intensities of the CG and TA independent selections and the mutual inhibition relationship. Besides, by the evolution mechanism of genomes, we speculated the evolution modes of prokaryotes in mild and extreme environments in the anaerobic age and the evolving process of prokaryotes from anaerobic to aerobic environment on earth as well as the originations of different eukaryotes.
conclusionWe found that there are two independent selection modes in genome sequences. The evolution of genome sequence is determined by the two independent selection modes and the mutual inhibition relationship between them.
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