| Computational molecular biology is a new interdisciplinary subject. It is based on the computer and the network as a tool, and it applies mathematics, chemistry, physics and information science theory and the research method of DNA, RNA and protein into domain. Research in computational molecular biology can help us to further explore the major problems of biological evolution and the mystery of life.Comparative analysis of biological sequence analysis is generally divided into two categories and it is comparison method and non alignment method. In recent years, non alignment analysis method as comparison supplement and development makes more and more researchers’favor, and become a hot topic of research point in computational molecular biology domain. This article is researching on the similarity of biological sequences with Burrows-Wheeler algorithm technology,and then construct the phylogenetic tree,and then obtain the valuable information.The main work of this paper includes the following two aspects:1、According to the chemical structure of nucleotide A, T, C, G, and then classifying them into two members,and the members are Y and R,the Y means pyrimidine and the R means purine, in other words, Y={C, T} and R={A, G}; similar to the four nucleotide base be classified as follows:M means keto, K means amino:M={A. C} and K={G, T}; W is weak hydrogen bonds. S is a strong hydrogen bond, W={A, T} and S={C. G}. Based on YR, MK and WS sequence and by using the extended Burrows-Wheeler algorithm and Burrows-Wheeler similarity distribution, and then it can get a new method to compare the DNA sequence, to using this method can make a similarity comparison for the HA fragment of DNA sequence of80kinds of H5NI avian influenza virus, and reconstruction of phylogenetic tree, make a comprehensive analysis of the evolutionary relationship between different areas and different host of avian influenza H5N1virus, the obtained of results are dictionary order more biological significance. Through the analysis of the similarity relationship between avian influenza virus, it can provide the theoretical basis for studying on the characteristics of regional spread of bird flu.2, According to the relative properties of protein’s two level structure and chemical properties of amino acids,we classify the amino acids into four categories:non-polar, hydrophobic, Z={L, M, W, I, V, F, Y}; the volume is small, the non polarity, B={P, G); hydrophilic, take charge, polarity, X={C, T, H, S, N, D}; the other, J={Q, A. E. K. R}. the protein sequence into character sequences of four characters Z, B, X and J, then based on Z, B. X, J sequence by using the extended Burrows Wheeler algorithm and Burrows Wheeler similarity distribution, new method analysis of the protein sequence, and this method is applied to13β-globin sequences similarity comparison of protein sequences, and construct the phylogenetic tree, using this method, and compared the transferrin gene in24vertebrates, better results were obtained. Change the protein sequence into four character sequences,it is Z, B, X and J, and then it is based on Z, B, X, J sequence by using the extended Burrows-Wheeler algorithm and Burrows Wheeler similarity distribution, then get a new method for the analysis of protein sequences obtained, and this method is applied into13β-globin sequences of similarity comparison of protein sequences, and constructing the phylogenetic tree, to use this method and compare the transferrin gene in24vertebrates, we can get a better results. |
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