Structural Matrix Is Applied In Comparison Of Similarity For Biological Sequences

According to the characterization of DNA primary sequence, DNA primary sequences are transformed into numeric sequences called disperse time sequence of DNA primary sequence by representing A, T, G and C, as 1, 2, 3 and 4. The protein is also the linear macro-molecule as same as DNA and RNA. It is character string of character set N={A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y}. The protein sequence's comparison is not only comparison of string character, but must consider their chemical constitution and the chemical property. They are divided into four kinds according to chemical properties of 20 kinds of amino acids as well as the protein secondary structure. Namely, hydrophilicity , polarity, electrically charged X=HPC={D, N, S, H, T, C}, hydrophobicity, nonpolarity Z=HA={Y, F, V, I, W, M, L}, nonpolarity and small B=AS={G, P}, others J=O={R, K, E, A, Q}. In a similar way, according to the characterization of primary protein sequence, protein primary sequences are transformed into numeric sequences called disperse time sequence of protein primary sequence by representing X, Z, B, J as 1, 2, 3, 4.Based on which this paper employs the matrix to represent the structure of DNA and protein primary sequence in nature. The authors propose structural matrix, build up a DNA and protein primary sequence model based on structural matrix, and carry through the similarity research on DNA and protein primary sequence, to find a reasonable value for similarity assessment. Furthermore, transformation on matrix enhances the adaptability of the model.