Legacy Genomic codon usage Computational Demonstration and Data: Depreciated
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| _version_ | 1866901948806987776 |
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| author | Moore, Douglas Joseph Huntington |
| author_facet | Moore, Douglas Joseph Huntington |
| contents | <p><strong>Genomic codon usage reveals First-Classness: Computational Demonstration and Data</strong></p> <p>This deposit contains Iteration 1 of the Genetic Code Analysis project. The aim of this iteration is to establish, in a fully reproducible and operational manner, the structural organisation of the standard genetic code as revealed through codon-orbit structure and First-Classness (FC) measures, independently of chemical or biochemical interpretation.</p> <p>Using aggregated RefSeq codon-usage data drawn from 70,425 species, the included pipeline computes ENC and FC compliance metrics across the full dataset and generates the figures reported in the accompanying paper. The core FC compliance metric — the ratio of within-orbit to between-orbit codon-usage variance — is evaluated against a 10,000-permutation null model, yielding the Z-score and empirical P-value reported in the manuscript. An orbit-by-orbit analysis characterises FC compliance across all 21 degeneracy families, demonstrating a systematic structural gradient consistent with the mathematical constraints of the κ/ρ orbit framework. A Serine/Leucine tension analysis and a paired ciliate nuclear/mitochondrial comparison are included as auxiliary analyses corroborating the primary structural result.</p> <p> </p> <p>This package has been depreciated and replaced with a cut down version for publication</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_18648827 |
| institution | Zenodo |
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| publishDate | 2026 |
| publisher | Zenodo |
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| spellingShingle | Legacy Genomic codon usage Computational Demonstration and Data: Depreciated Moore, Douglas Joseph Huntington genetic code genetic code degeneracy 64-to-20 mapping codon structure codon symmetry codon orbits κ/ρ orbit structure dihedral group action computational biology bioinformatics comparative genomics GenBank RefSeq codon usage analysis first-classness structural biology mathematical biology foundations of biology non-standard genetic code analysis computational demonstration Computational Biology Bioinformatics Theoretical Biology Mathematical Biology Genomics Foundations of Science Applied Mathematics Discrete Mathematics Group Theory (Applications) Philosophy of Biology <p><strong>Genomic codon usage reveals First-Classness: Computational Demonstration and Data</strong></p> <p>This deposit contains Iteration 1 of the Genetic Code Analysis project. The aim of this iteration is to establish, in a fully reproducible and operational manner, the structural organisation of the standard genetic code as revealed through codon-orbit structure and First-Classness (FC) measures, independently of chemical or biochemical interpretation.</p> <p>Using aggregated RefSeq codon-usage data drawn from 70,425 species, the included pipeline computes ENC and FC compliance metrics across the full dataset and generates the figures reported in the accompanying paper. The core FC compliance metric — the ratio of within-orbit to between-orbit codon-usage variance — is evaluated against a 10,000-permutation null model, yielding the Z-score and empirical P-value reported in the manuscript. An orbit-by-orbit analysis characterises FC compliance across all 21 degeneracy families, demonstrating a systematic structural gradient consistent with the mathematical constraints of the κ/ρ orbit framework. A Serine/Leucine tension analysis and a paired ciliate nuclear/mitochondrial comparison are included as auxiliary analyses corroborating the primary structural result.</p> <p> </p> <p>This package has been depreciated and replaced with a cut down version for publication</p> |
| title | Legacy Genomic codon usage Computational Demonstration and Data: Depreciated |
| topic | genetic code genetic code degeneracy 64-to-20 mapping codon structure codon symmetry codon orbits κ/ρ orbit structure dihedral group action computational biology bioinformatics comparative genomics GenBank RefSeq codon usage analysis first-classness structural biology mathematical biology foundations of biology non-standard genetic code analysis computational demonstration Computational Biology Bioinformatics Theoretical Biology Mathematical Biology Genomics Foundations of Science Applied Mathematics Discrete Mathematics Group Theory (Applications) Philosophy of Biology |
| url | https://doi.org/10.5281/zenodo.18648827 |