Estimating the "Effective number of codons": The Wright way of determining codon homozygosity leads to superior estimates
Estimating the "Effective number of codons": The Wright way of determining codon homozygosity leads to superior estimates
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DOI：
10.1534/genetics.105.049643
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发表时间：
2006-02-01
期刊：
影响因子：
3.3
通讯作者：
Fuglsang, A
中科院分区：
文献类型：
--
作者：
Fuglsang, A
1990年，Frank Wright提出了一种通过估算“有效密码子数”（N-c）来测量基因中同义密码子使用偏好的方法。最近已经进行了几次尝试来改进赖特对N-c的估计，但是在基因编码的蛋白质不包含具有简并密码子的所有氨基酸的情况下起作用的方法还没有相互测试。在这篇文章中，我得到了五个新的估计N-C和测试他们一起公布的两个估计，在严格的测试条件下使用rescue。密码子纯合性E的估计是N-c估计的关键。F可以用两种密切相关的方法来估计，对应于有或没有替换的采样，后者是赖特使用的。基于无替换抽样的N-c方法在短基因长度下的准确性比基于有替换抽样的N-c方法要好得多，这表明Wright的纯合性方法更优越。上级。令人惊讶的是，基于替换取样的方法显示出与大肠杆菌中mRNA水平的上级相关性。
In 1990, Frank Wright introduced a method for measuring synonymous codon usage bias in a gene by estimation of the "effective number of codons," N-c. Several attempts have been made recently to improve Wright's estimate of N-c, but the methods that work in cases where a gene encodes a protein not containing all amino acids with degenerate codons have not been tested against each other. In this article I derive five new estimators of N-c and test them together with the two published estimators, using resampling under rigorous testing conditions. Estimation of codon homozygosity, E, turns out to he a key to the estimation of N-c. F can be estimated in two closely related ways, corresponding to sampling with or without replacement, the latter being what Wright used. The N-c methods that are based on sampling without replacement showed Much better accuracy at short gene lengths than those based on sampling with replacement, indicating that Wright's homozygosity method is superior. Surprisingly, the methods based on sampling with replacement displayed a Superior correlation with mRNA levels in Escherichia coli.