Codon Usage Bias #

What is Codon Usage bias (CB) #

Preferential use of synonymous codons/codons in the translational process is known as ‘codon usage bias’ or simply ‘codon bias’.

Synonymous codons #

The different codons that code the same amino acid are called ‘synonymous codons’.

Optimized codons #

A gene is highly biased in specific codon usage pattern to synthesis specific amino acid in a protein is often referred as “optimized codons” or “frequent codons”. Its mainly contribute to the “translational selection”.

Codon degeneracy #

More than one codon used to code for single amino acid residues in the protein is called as ‘degeneracy’ of the codons

Major factor for codon bias #

 Mutation

 Codon selection

 Random genetic drift

 Recombination

Codon bias quantifying methods #

 Codon bias indices

 Codon preference bias

 Chi-squared approach

 P2 index

 Frequency of optimal codons

 Relative synonymous codon usage

 Codon adaptation index

 Effective numbers of codons

 Synonymous codon usage order

 Codon correspondence analysis

 Codon context analysis

List of computational tools #

Reference #

1. Behura, S. K. & Severson, D. W. 2013. Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes. Biological Reviews, 88, 49-61.

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