Zhang Zhenguo, Sablok Gaurav
Department of Biology, University of Rochester, River Campus Box 270211, Rochester, NY, 14627, USA.
Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, IASMA, 380010, Italy.
Methods Mol Biol. 2018;1667:139-148. doi: 10.1007/978-1-4939-7278-4_11.
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.
核糖体每次通过读取三核苷酸（即密码子）将一个氨基酸添加到正在生长的肽链上。20种氨基酸通常由61个密码子编码，因此一种氨基酸可以由多个密码子编码，编码相同氨基酸的密码子被称为同义密码子。有趣的是，同义密码子的使用往往不均衡：在一个基因组中，有些密码子的使用频率高于其替代密码子。密码子使用的不均衡被称为密码子使用偏好（CUB）。CUB广泛存在，其成因和后果一直是深入研究的对象。为便于研究CUB，在本章中我们介绍一种使用免费软件密码子使用分析器估计CUB的方法，并以二穗短柄草为例进行应用。要完成这个方法，读者需要一些基本的命令行技能。简而言之，该方法包括四个主要步骤：下载数据和软件、设置计算环境、准备数据以及估计CUB。
