密码子使用偏性量化方法研究综述

Review and Prospect of the Principle and Methods Quantifying Codon Usage Bias

在基因组学水平上研究密码子使用偏性模式、成因并分析进化过程中的选择压力在基因组学研究中有重要意义。文章概述了目前提出的密码子使用偏性的量化方法及实现原理。目前研究发现:有些量化密码子偏性的方法受高表达基因参考数据集未完全注释的限制,不同密码子位置对变异和选择的影响不同,以及不同密码子位置处GC含量和嘌呤含量的贡献不同。由此展望密码子偏性量化方法发展方向为:需要设计不需要相关参考基因集合先验知识的密码子使用偏性量化方法;考虑不同位置处背景核苷酸组成的密码子使用偏性的量化方法;同时考虑基因表达水平的密码子使用偏性量化方法。最后,归纳了目前可用的密码子使用偏性的量化工具和数据库。

Genome-wide investigations of codon bias patterns, their causes and consequences, and identifying se- lective forces that shape their evolution are significant in studies of genome biology. We outline different principles and methods of measurement of codon usage bias （CUB）. The former measures are highly dependent on their corre- sponding reference sets （from which preferred codons are derived） and accordingly are limited by the comprehen- siveness and accuracy of reference sets. in addition to GC content, purine content is also a significant feature of background nucleotide composition 03NC）. So we should provide means that incorporates GC content of coding se- quence as BNC into CUB estimation. At last, We have compiled a list of computer algorithms and software available for estimating codon bias.