拟密码子适应指数方法的设计及应用  

Design and Application of Quasi-codon Adaptation Index Method

作　　者：马冲 祖颖 朱平[1] MA Chong;ZU Ying;ZHU Ping(School of Science, Jiangnan University, Wuxi 21d122, Jiangsu, China)

机构地区：[1]江南大学理学院,中国江苏无锡214122

出　　处：《生命科学研究》2018年第2期122-128,共7页Life Science Research

基　　金：国家自然科学基金资助项目(11271163)

摘　　要：密码子适应指数(codon adaptation index,CAI)测量的是生物体内某个基因所用密码子与高表达基因所用密码子的相符合程度,是反映密码子偏好性的一个重要指标。文章根据拟氨基酸编码方法首次提出拟密码子适应指数(quasi-codon adaptation index,Q-CAI)。首先,通过氨基酸编码方法,得到密码子使用具有偏好性,并运用MATLAB分析其碱基组成,发现醋酸菌、大肠杆菌和双歧杆菌的密码子偏好使用c/g结尾,GC整体含量也比较高。随后,利用CAI模型方法进一步证明密码子具有偏好性。最后,利用文中提出的Q-CAI方法,得到醋酸菌、大肠杆菌和酵母菌所有序列的Q-CAI运算结果,发现它们都比CAI运算结果数值更高、更明显,而且双歧杆菌、枯草杆菌和链球菌的Q-CAI运算结果也普遍比CAI运算结果数值高,说明Q-CAI方法能更有效地评价密码子偏好性。文中所使用的6个单细胞物种的90条序列是从NCBI中下载,分析结果说明了Q-CAI方法比CAI方法更具有优越性,是衡量密码子偏好性的有效方法,对研究物种的基因突变有重要参考意义。The codon adaptation index （CAI）, an important indicator of codon preference, measures the degree of codification between codons used by a gene and the corresponding highly expressed one. Here, the quasieodon adaptation index （Q-CAI） was proposed according to the coding method of quasi-amino acids. Firstly, the amino acid coding method was used to obtain the codon usage preference, and the base composition was analyzed by the MATLAB. It was found that acetic acid bacteria, Escherichia coli and Bifidobacterium pre- fer the c/g-end codons, and have a relatively high GC content. Secondly, using the CAI model method, the experimental results further proved that the codons have preferences. Finally, the Q-CAI results of all the sequences of acetic acid bacteria, E. coli and yeast were obtained by the Q-CAI method, and were found to be higher and more pronounced. And the Q-CAI results of Bifidobacterium, Bacillus subtilis and Streptococcus were generally higher than those of CAI. These meant Q-CAI method could more effectively evaluate the codon preference. The 90 sequences of the six single-celled species used in this article were download- ed from NCBI. The analysis on them showed that the Q-CAI method is more advantageous than the CAI method and is an effective method to measure the codon preference. It would be of great significance in study of gene mutation.

关 键 词：密码子适应指数(CAI) 拟氨基酸编码方法 拟密码子适应指数(Q-CAI) 密码子偏好性 同义密码子相对使用度(RSCU) 

分 类 号：Q812[生物学—生物工程] TP399[自动化与计算机技术—计算机应用技术]