New Methods Of Analyzing Avian Influenza Virus Sequences

The primary structures of DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are all macro molecules which are unbranched polymers built up from smaller units. In the case of DNA, these units are the four nucleotide residues A (adenine), C (cytosine), G (guanine) and T (thymine), while for RNA, the units are the four nucleotide residues A, C, G and U(uracil). Thus, a DNA (RNA) sequence can be identified with a word over the alphabet (A, C, G, T (U)), and a protein sequence can be taken as a string over twenty letters. So the tools and methods in Combinatorics and Statistics will play important roles in studying the similarity of avian influenza virus sequences. Also, we can use method of geometry and algebra to study the AIVs.The main contents as listed as follows:In Chapter 1, we introduce the overview of avian influenza virus and Bio informatics. Most of the terms and concepts used in this paper are explained briefly here.In Chapter 2, we consider a new matrix representation of DNA sequences to H5N1 and their numerical characterization.In Chapter 3, we consider a new curve mapping of protein sequences to H5N1 and their numerical characterization.In Chapter 4, based on the matrix representation of DNA sequences, we calculate the new invariant. Based on the new invariant, we calculate the similarity matrix of the HA segment of 80 different H5N1 species. Based on the new curve mapping of protein sequences, we also calculate the new invariant and the similarity matrix of 123 different H5N1 species. Based on these similarity matrices, we construct phylogenetic trees respectively, and we analyze phylogenetic relationships of them.In Chapter 5, we give the conclusion and prospect.