Abstract: Based on three physical and chemical properties of twenty kinds of amino acids, a three-dimensional graphical representation of protein sequences was proposed in order to compare the similarity of protein sequences. Furthermore, the graphical representation curve was characterized by the mathematical descriptor. Then, the similarity analysis based on the mathematical descriptors of protein sequences was given for the mitochondrial NADH dehydrogenase protein sequences of nine different species．

Key words: protein sequences, graphical representation, mathematical descriptor, similarity analysis