ArticleGenomics, proteomics & bioinformatics2011
On the organizational dynamics of the genetic code.
Article in Genomics, proteomics & bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 22 citations in OpenAlex.
- Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades.Genomics, proteomics & bioinformatics · 2020Article
- GC content of vertebrate exome landscapes reveal areas of accelerated protein evolution.BMC evolutionary biology · 2019Article
- Interplay between coding and exonic splicing regulatory sequences.Genome research · 2019Article
- Randomness in Sequence Evolution Increases over Time.PloS one · 2016Article
- Ribogenomics: the science and knowledge of RNA.Genomics, proteomics & bioinformatics · 2014Article
- Does the genetic code have a eukaryotic origin?Genomics, proteomics & bioinformatics · 2013Article
- The pendulum model for genome compositional dynamics: from the four nucleotides to the twenty amino acids.Genomics, proteomics & bioinformatics · 2012Article
- Life on two tracks.Genomics, proteomics & bioinformatics · 2012Article
- Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance.BMC bioinformatics · 2012Article
- Replication-Associated Mutational Pressure (RMP) Governs Strand-Biased Compositional Asymmetry (SCA) and Gene Organization in Animal Mitochondrial Genomes.Current genomics · 2012Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The organization of the canonical genetic code needs to be thoroughly illuminated. Here we reorder the four nucleotides-adenine, thymine, guanine and cytosine-according to their emergence in evolution, and apply the organizational rules to devising an algebraic representation for the canonical genetic code. Under a framework of the devised code, we quantify codon and amino acid usages from a large collection of 917 prokaryotic genome sequences, and associate the usages with its intrinsic structure and classification schemes as well as amino acid physicochemical properties. Our results show that the algebraic representation of the code is structurally equivalent to a content-centric organization of the code and that codon and amino acid usages under different classification schemes were correlated closely with GC content, implying a set of rules governing composition dynamics across a wide variety of prokaryotic genome sequences. These results also indicate that codons and amino acids are not randomly allocated in the code, where the six-fold degenerate codons and their amino acids have important balancing roles for error minimization. Therefore, the content-centric code is of great usefulness in deciphering its hitherto unknown regularities as well as the dynamics of nucleotide, codon, and amino acid compositions.
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Registered trials
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