Oct 19, 2017

Estimate Codon Usage Bias Using Codon Usage Analyzer (CUA)

Methods in Molecular Biology
Zhenguo Zhang, Gaurav Sablok

Abstract

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.

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Mentioned in this Paper

Computer Software
Exons
Genome
Amino Acids, I.V. solution additive
Environment
Transfer RNA
Gene Expression
Computer Programs and Programming
Sense Codon
Codon Genus

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