Abstract: Using the information of Chaos game representation of protein（PCGR），there is a new method to align two protein sequences.According to the distance of PCGR points between that two sequences，it could find all local segments of them without comparing the sequences amino acid by amino acid.The alignment data are described in dot matrix plots，which demonstrate the homology of two sequences and display all the similar segments between them.It maybe not a more efficient programmer，but it has a better procedure input，PCGR points，a new powerful protein sequences alignment.

Key words: chaos game representation of protein, sequence alignment of protein, classification of amino acid

摘要： 利用蛋白质混沌游走表示法（PCGR）提出一种新的蛋白质序列比对方法。通过计算两序列之间的PCGR点距离，就可以找到所有的局部相似片断。根据氨基酸的化学物理性质把氨基酸分成4和7类，针对分类与无分类的各种情况进行蛋白质序列比对。为了更直观地描述比对结果，采用点阵图来表示比对数据，不仅能显示两序列间所有相同片断，还可以体现出序列的相似性。

关键词: 蛋白质混沌游走表示法, 蛋白质序列比对, 氨基酸分类