ArticleBiology direct2010
Modeling compositional dynamics based on GC and purine contents of protein-coding sequences.
Article in Biology direct, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 15 citations in OpenAlex.
- Laws of Genome Nucleotide Composition.Genomics, proteomics & bioinformatics · 2024Article
- The Shift in Synonymous Codon Usage Reveals Similar Genomic Variation during Domestication of Asian and African Rice.International journal of molecular sciences · 2022Article
- CompoDynamics: a comprehensive database for characterizing sequence composition dynamics.Nucleic acids research · 2022Article
- Thermodynamic and kinetic stability of the Josephin Domain closed arrangement: evidences from replica exchange molecular dynamics.Biology direct · 2017Article
- Quantitative analysis of correlation between AT and GC biases among bacterial genomes.PloS one · 2017Article
- 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
- 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
- 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
- On the molecular mechanism of GC content variation among eubacterial genomes.Biology direct · 2012Article
- The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia) reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria.BMC evolutionary biology · 2011Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundUnderstanding the compositional dynamics of genomes and their coding sequences is of great significance in gaining clues into molecular evolution and a large number of publically-available genome sequences have allowed us to quantitatively predict deviations of empirical data from their theoretical counterparts. However, the quantification of theoretical compositional variations for a wide diversity of genomes remains a major challenge.
resultsTo model the compositional dynamics of protein-coding sequences, we propose two simple models that take into account both mutation and selection effects, which act differently at the three codon positions, and use both GC and purine contents as compositional parameters. The two models concern the theoretical composition of nucleotides, codons, and amino acids, with no prerequisite of homologous sequences or their alignments. We evaluated the two models by quantifying theoretical compositions of a large collection of protein-coding sequences (including 46 of Archaea, 686 of Bacteria, and 826 of Eukarya), yielding consistent theoretical compositions across all the collected sequences.
conclusionsWe show that the compositions of nucleotides, codons, and amino acids are largely determined by both GC and purine contents and suggest that deviations of the observed from the expected compositions may reflect compositional signatures that arise from a complex interplay between mutation and selection via DNA replication and repair mechanisms.
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