The architecture of the genome integrates scale independence with inverse symmetry
The simplest building blocks of the genome, the k-mers, show two properties that are widely observed. Their frequency distribution is scale-free (a variant Zipfian distribution), and the inverse symmetry of k-mers is observable on the same strand. These phenomena are linked; Watson–Crick...
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2025-04-01
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| Series: | Academia Molecular Biology and Genomics |
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| author | Greg Warr Les Hatton |
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The simplest building blocks of the genome, the k-mers, show two properties that are widely observed. Their frequency distribution is scale-free (a variant Zipfian distribution), and the inverse symmetry of k-mers is observable on the same strand. These phenomena are linked; Watson–Crick base pairing generates inverse symmetry (IS) under the condition that the same frequency distribution of k-mers is present on both strands of the genome. A stable scale-free equilibrium distribution of k-mer frequency in all genomes is predicted by a purely probabilistic theory, the Conservation of Hartley–Shannon Information (CoHSI). This does not replace the diverse mechanism-based explanations of IS that have been advanced, but in principle, it aggregates all operative mechanisms. CoHSI predicts that both the scale-free distribution of k-mers and the IS that follows from it should decay gradually and stochastically as the genome size decreases and the length of the k-mers increases. These predictions were tested in 178 genomes from all domains of life and viruses. The precision of both the Zipfian distribution of k-mer frequency and of IS decayed progressively as the genome size decreased and k-mer length increased, regardless of the structure of the genome; DNA or RNA, nuclear or plastid, double- or single-stranded. No clear partition into IS-compliant and non-compliant genomes could be inferred. These results suggest that both IS and scale-free distributions of k-mer frequency in genomes are linked properties that emerge probabilistically and in a mechanism-agnostic manner across the three domains of life and viruses. |
| format | Article |
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| institution | Kabale University |
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| language | English |
| publishDate | 2025-04-01 |
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| spelling | doaj-art-2d2ec515b28c406d93a18fbfb5a205362025-08-20T03:25:22ZengAcademia.edu JournalsAcademia Molecular Biology and Genomics3064-97652025-04-012210.20935/AcadMolBioGen7650The architecture of the genome integrates scale independence with inverse symmetryGreg Warr0Les Hatton1Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29403, USA.School of Computer Science and Mathematics, Kingston University, London KT1 1LQ, UK. The simplest building blocks of the genome, the k-mers, show two properties that are widely observed. Their frequency distribution is scale-free (a variant Zipfian distribution), and the inverse symmetry of k-mers is observable on the same strand. These phenomena are linked; Watson–Crick base pairing generates inverse symmetry (IS) under the condition that the same frequency distribution of k-mers is present on both strands of the genome. A stable scale-free equilibrium distribution of k-mer frequency in all genomes is predicted by a purely probabilistic theory, the Conservation of Hartley–Shannon Information (CoHSI). This does not replace the diverse mechanism-based explanations of IS that have been advanced, but in principle, it aggregates all operative mechanisms. CoHSI predicts that both the scale-free distribution of k-mers and the IS that follows from it should decay gradually and stochastically as the genome size decreases and the length of the k-mers increases. These predictions were tested in 178 genomes from all domains of life and viruses. The precision of both the Zipfian distribution of k-mer frequency and of IS decayed progressively as the genome size decreased and k-mer length increased, regardless of the structure of the genome; DNA or RNA, nuclear or plastid, double- or single-stranded. No clear partition into IS-compliant and non-compliant genomes could be inferred. These results suggest that both IS and scale-free distributions of k-mer frequency in genomes are linked properties that emerge probabilistically and in a mechanism-agnostic manner across the three domains of life and viruses.https://www.academia.edu/128851197/The_architecture_of_the_genome_integrates_scale_independence_with_inverse_symmetry |
| spellingShingle | Greg Warr Les Hatton The architecture of the genome integrates scale independence with inverse symmetry Academia Molecular Biology and Genomics |
| title | The architecture of the genome integrates scale independence with inverse symmetry |
| title_full | The architecture of the genome integrates scale independence with inverse symmetry |
| title_fullStr | The architecture of the genome integrates scale independence with inverse symmetry |
| title_full_unstemmed | The architecture of the genome integrates scale independence with inverse symmetry |
| title_short | The architecture of the genome integrates scale independence with inverse symmetry |
| title_sort | architecture of the genome integrates scale independence with inverse symmetry |
| url | https://www.academia.edu/128851197/The_architecture_of_the_genome_integrates_scale_independence_with_inverse_symmetry |
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