Phylogenetic Study Of Baculovirus Genome Based On Markov Model

In baculovirus, numerous conserved genes have very important biological functions, and they are important roles in virus evolution and classification. Therefore, proteomic analysis of the all baculovirus based on the method of k-string is an interesting work for research of classification of these baculovirus.In the second chapter, according to the Markov Model, we predict the expected frequency of the 4-string for the 30 baculovirus proteome based on the Markov Model. We scan the actual frequency of these 4-string and calculate the relative abundance of a 4-string for each baculovirus proteome. Then, we construct vector based on the relative frequency and the actual frequency of these 4-string, respectively, to character these baculovirus proteome. According to the defining distance between of the vectors, we obtain the similarities of 30 baculovirus, and analyze their evolution and classification. Our conclusion are almost consistent with the biological evolution relationship, And we point out that the conclusion based on the relative frequency of these 4-string is better than the results based on the actual frequency of these 4-string.In the third and fourth chapter, we find out the proteins, which the most actual frequency 4-string or the greatest relative frequency 4-string occurs in these proteins. And, the functions of these proteins are analyzed to illustrate the role of these 4-tring from the five groups of baculovirus. And the phylogenetic tree of 30 baculovirus are constructed according to the distance matrix based on the actual frequency and relative frequency of 4-string.In the fifth chapter, we present a new method for the similarity analysis of biological sequences. Taking the ND5 protein of nine species as an example, we firstly show the effectiveness of our method. Then, applying the method to lef-8 gene in all baculovirus, the phylogenetic tree of 30 baculovirus is obtained, which is almost consistent with the biology taxonomy.