The 'effective number of codons' revisited
The 'effective number of codons' revisited
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DOI：
10.1016/j.bbrc.2004.03.138
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发表时间：
2004-05-07
影响因子：
3.1
通讯作者：
Fuglsang, A
中科院分区：
文献类型：
--
作者：
Fuglsang, A
Frank Wright [Gene 87（1990）23]基于密码子纯合性推导出用于计算称为“有效密码子数”（（N）除以capc）的量的公式。这个数量是20和61之间的数字，并告诉基因中密码子使用的偏向程度。即，对于极端偏向的基因，它接近20个密码子，对于没有偏好地使用所有可能的密码子的基因，它接近61个密码子。在密码子偏好性（N）的不同度量中，相对于capc被认为是最有用的，并且在处理密码子使用现象的论文中得到了广泛的使用。本文讨论了密码子纯合性和（N）over capc的数学性质。使用大肠杆菌作为模式生物。结果表明，在存在偏差的情况下，（N）/capc的经典计算公式可以适当地替代，当简并性组内的一个氨基酸（或多个氨基酸）与强密码子偏好性相关，而同时同一简并性组中的其它氨基酸几乎没有偏好性时。提出了一种称为（N）over capc* 的替代估计，并与（N）over capc进行了测试，并且在存在这种偏差时表现得更好。(C)2004年爱思唯尔公司All rights reserved.
Frank Wright [Gene 87 (1990) 23] derived a formula for calculation of a quantity termed the 'effective number of codons' ((N) over capc) based on codon homozygosities. This quantity is a number between 20 and 61 and tells to what degree the codon usage in a gene is biased. i.e.. it approaches 20 codons for the extremely biased genes, and approaches 61 for the genes where all possible codons are used with no preference. Among the different measures of codon bias (N) over capc is considered the most useful and has found widespread use in papers dealing with codon usage phenomena. In this paper, the mathematical behaviours of codon homozygosities and (N) over capc are evaluated. using Escherichia coli as the model organism. The results indicate that the classical formula for calculation of (N) over capc Could appropriately be substituted under circumstances, where there is bias discrepancy, i.e., when one amino acid (or more) within a degeneracy group is associated with strong codon bias while at the same time others in the same degeneracy group have little bias. An alternative estimator termed (N) over capc*, is proposed and tested against (N) over capc, and performs better when there is such bias discrepancy. (C) 2004 Elsevier Inc. All rights reserved.