生命科学研究2018，Vol.22Issue(2)：122-128,7.DOI:10.16605/j.cnki.1007-7847.2018.02.005
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
摘要
Abstract
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 quasicodon 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 prefer 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 Strepto-coccus 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)Key words
codon adaptation index (CAI)/quasi-amino acid coding method/quasi-codon adaptation index (Q-CAI)/codon preference/relative synonymous codon usage (RSCU)分类
生物科学引用本文复制引用
马冲,祖颖,朱平..拟密码子适应指数方法的设计及应用[J].生命科学研究,2018,22(2):122-128,7.基金项目
国家自然科学基金资助项目(11271163) （11271163）
