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Codon usage bias in Physcomitrella patens. Codon usage bias refers to differences in the frequency of occurrence of synonymous codons in coding DNA.A codon is a series of three nucleotides (a triplet) that encodes a specific amino acid residue in a polypeptide chain or for the termination of translation (stop codons).
Effective number of codons (abbreviated as ENC or Nc) is a measure to study the state of codon usage biases in genes and genomes. [1] The way that ENC is computed has obvious similarities to the computation of effective population size in population genetics. [2]
A common idea in the literature of molecular evolution is that codon usage and genome composition reflect the effects of mutation bias, e.g., codon usage has been treated with a mutation-selection-drift model combining mutation biases, selection for translationally preferred codons, and drift.
The Codon Adaptation Index (CAI) [1] is the most widespread technique for analyzing codon usage bias.As opposed to other measures of codon usage bias, such as the 'effective number of codons' (Nc), which measure deviation from a uniform bias (null hypothesis), CAI measures the deviation of a given protein coding gene sequence with respect to a reference set of genes.
The frequency of codons, also known as codon usage bias, can vary from species to species with functional implications for the control of translation. The codon varies by organism; for example, most common proline codon in E. coli is CCG, whereas in humans this is the least used proline codon. [53]
Such codon usage bias may arise for different reasons, some selective, and some neutral. In Saccharomyces cerevisiae synonymous codon usage has been shown to influence mRNA folding stability, with mRNA encoding different protein secondary structure preferring different codons. [9]
Codon usage bias, a measure related to codon frequencies, was one of the first detection methods used in methodical assessments of HGT. [16] This approach requires a host genome which contains a bias towards certain synonymous codons (different codons which code for the same amino acid) which is clearly distinct from the bias found within the ...
This is reflected in the codon usage bias that is observed in many species. Mutations that cause the altered codon to produce an amino acid with similar functionality ( e.g. a mutation producing leucine instead of isoleucine ) are often classified as silent; if the properties of the amino acid are conserved, this mutation does not usually ...