Estimate Codon Usage Bias Using Codon Usage Analyzer (CUA).

One amino acid is added to a growing peptide by a ribosome through reading triple nucleotides, i.e., a codon, each time. Twenty species of amino acids are often coded by 61 codons, so one amino acid can be coded by more than one codon and the codons coding the same amino acid are called synonymous. Intriguingly, synonymous codons' usage is often uneven: some are used more often than their alternatives in a genome. The unevenness of codon usage is termed codon usage bias (CUB). CUB is widespread, and its causes and consequences have been under intensive investigation. To facilitate the studying of CUB, in this chapter we present a protocol of estimating CUB by using the free software Codon Usage Analyzer, and apply it to Brachypodium distachyon as an example. To accomplish this protocol, the readers need some basic command-line skills. Briefly, the protocol comprises four major steps: downloading data and software, setting up computing environment, preparing data, and estimating CUB.