Wright F
Institute of Animal Genetics, University of Edinburgh, U.K.
Gene. 1990 Mar 1;87(1):23-9. doi: 10.1016/0378-1119(90)90491-9.
A simple measure is presented that quantifies how far the codon usage of a gene departs from equal usage of synonymous codons. This measure of synonymous codon usage bias, the 'effective number of codons used in a gene', Nc, can be easily calculated from codon usage data alone, and is independent of gene length and amino acid (aa) composition. Nc can take values from 20, in the case of extreme bias where one codon is exclusively used for each aa, to 61 when the use of alternative synonymous codons is equally likely. Nc thus provides an intuitively meaningful measure of the extent of codon preference in a gene. Codon usage patterns across genes can be investigated by the Nc-plot: a plot of Nc vs. G + C content at synonymous sites. Nc-plots are produced for Homo sapiens, Saccharomyces cerevisiae, Escherichia coli, Bacillus subtilis, Dictyostelium discoideum, and Drosophila melanogaster. A FORTRAN77 program written to calculate Nc is available on request.
本文提出了一种简单的方法，用于量化基因密码子使用情况与同义密码子均等使用情况的偏离程度。这种同义密码子使用偏好性的度量方法，即“基因中使用的有效密码子数”Nc，仅根据密码子使用数据即可轻松计算得出，且与基因长度和氨基酸组成无关。Nc的取值范围为20（在极端偏好情况下，每个氨基酸仅使用一个密码子）到61（当使用替代同义密码子的可能性相同时）。因此，Nc为基因中密码子偏好程度提供了一个直观且有意义的度量。通过Nc图可以研究不同基因间的密码子使用模式：即Nc与同义位点的G + C含量的关系图。文中给出了人类、酿酒酵母、大肠杆菌、枯草芽孢杆菌、盘基网柄菌和黑腹果蝇的Nc图。如有需要，可提供一个用于计算Nc的FORTRAN77程序。
