基于图能量的2D图形表示.pdfVIP

A Novel Method of 2D Graphical Representation for Proteins and Its Application Dandan Sun a , Chunrui Xu a , Yusen Zhang a,1 a School of Mathematics and Statistics, Shandong University at Weihai, Weihai 264209, China. (Received July 25, 2015) Abstract In this paper, we propose the graph energy of 20 amino acids and the 2D graphical representation of protein sequences based on six physicochemical properties of 20 amino acids and the relationship between them. Moreover, we could get a specific vector from the graphical curve of a protein sequence, and use this vector to calculate the distance between two sequences. This approach avoids considering the differences in length of protein sequences. Finally, we research the similarities/dissimilarities of ND5 and 36PDs using our method and get better results compared with ClustalX2. 1 Introduction As the number of biological sequences increases fast in the public databases because of the rapid development of sequencing techniques, how to infer the potential information of a large number of sequences effectively and accurately becomes a critical challenge in biological information. Therefore, many valid methods in information extraction from DNA, RNA or protein sequences are proposed [1-6]. We all know that proteins, encoded by DNA, determine the material basis of an organism’s anatomy and physiology. Thus, detecting the similarity of proteins is definitely important [7-9], especially considering the structure and function of proteins. Models of protein analysis can be divided into two classes: sequence alignment [10-12] and alignment-free sequence comparison. The former applies a score function to