基于密码子特征的蛋白质序列图形表示

Graphical representation of protein sequences based on codon features

根据密码子碱基位置特征和氨基酸的疏水性指数值,20种氨基酸被映射为3维空间中的向量,提出一种新的迭代函数关系将氨基酸序列转化为三维空间中的一条曲线,获得一种新的蛋白质图形表示方法。对蛋白质图形,利用闵可夫斯基距离刻画两个3维曲线之间的距离,依此推断蛋白序列之间的差异性和物种之间的进化关系。将该方法分别应用在9个物种的ND5蛋白和12个物种的β-珠蛋白序列分析中,所得结果与ClustalW方法的结果以及其他文献中的结果对比后证明该文方法有效可行。

Based on the position characteristics of basic group of the codon and hydrophobicity value of amino acids,20 kinds of amino acids were mapped to the vectors in the three-dimensional space.A new iterative function of different parameters was proposed to convert the amino acid sequence into a curve in three-dimensional space and a new graphical representation method of protein was obtained.For the protein graph,Minkowski distance was adopted to characterize the distance between two 3 D curves.The difference of protein sequences and evolutionary relationship among species were thus inferred.This method was applied in sequence analysis of ND5 proteins of 9 species andβ-globin proteins of 12 species.After the results gained were compared with the results of ClustalW method and the results in other literatures,the method proposed in this paper is feasible and effective.