ArticleGenomics, proteomics & bioinformatics2007
A content-centric organization of the genetic code.
Article in Genomics, proteomics & bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 18 citations in OpenAlex.
- CompoDynamics: a comprehensive database for characterizing sequence composition dynamics.Nucleic acids research · 2022Article
- Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades.Genomics, proteomics & bioinformatics · 2020Article
- A novel skew analysis reveals substitution asymmetries linked to genetic code GC-biases and PolIII a-subunit isoforms.DNA research : an international journal for rapid publication of reports on genes and genomes · 2016Article
- 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
- Replication-Associated Mutational Pressure (RMP) Governs Strand-Biased Compositional Asymmetry (SCA) and Gene Organization in Animal Mitochondrial Genomes.Current genomics · 2012Article
- On the organizational dynamics of the genetic code.Genomics, proteomics & bioinformatics · 2011Article
- Modeling compositional dynamics based on GC and purine contents of protein-coding sequences.Biology direct · 2010Article
- The rules of variation: amino acid exchange according to the rotating circular genetic code.Journal of theoretical biology · 2010Article
- A novel DNA sequence periodicity decodes nucleosome positioning.Nucleic acids research · 2008Article
- A scenario on the stepwise evolution of the genetic code.Genomics, proteomics & bioinformatics · 2007Article
Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The codon table for the canonical genetic code can be rearranged in such a way that the code is divided into four quarters and two halves according to the variability of their GC and purine contents, respectively. For prokaryotic genomes, when the genomic GC content increases, their amino acid contents tend to be restricted to the GC-rich quarter and the purine-content insensitive half, where all codons are fourfold degenerate and relatively mutation-tolerant. Conversely, when the genomic GC content decreases, most of the codons retract to the AU-rich quarter and the purine-content sensitive half; most of the codons not only remain encoding physico-chemically diversified amino acids but also vary when transversion (between purine and pyrimidine) happens. Amino acids with sixfold-degenerate codons are distributed into all four quarters and across the two halves; their fourfold-degenerate codons are all partitioned into the purine-insensitive half in favorite of robustness against mutations. The features manifested in the rearranged codon table explain most of the intrinsic relationship between protein coding sequences (the informational content) and amino acid compositions (the functional content). The renovated codon table is useful in predicting abundant amino acids and positioning the amino acids with related or distinct physico-chemical properties.
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