Amino Acid And Codon Evolution And Relevant Questions

In Bioinformatics, amino acid and codon evolution is nuclear problems of life origin. The codon usage bias is called "dialect" of genes or genomes, which is firmly connected with gene structure and function, as well as protein structure. Meanwhile, they are widely applied to gene expression, gene identification, searching for drug targets and studying structure and function of proteins. The two aspects are emphases of this thesis, the main contents of this thesis are listed as follows:In Chapter 2, based on the thought of stepwise subdivision of synonymous domains and the network structure of the genetic code, a new evolution model of amino avids is proposed. Meanwhile, by comparing the amino acid evolution order with that proposed in classical co-evolution theory, this thesis verifies the validity of co-evolution theory, and gives several suggestions about amino acid and codon evolution.In Chapter 3, based on the co-evolution theory and mutation frequencies between different bases in different codon positions, the optimal scheme to measure the asymmetry of codon usage ADCT is proposed, furthermore, its advantage in sequence comparison and gene recognition by computers is verified.In Chapter 4, this thesis proves the correlations of CAI with Shannon Entropy and Effective Number of Codons, it also proves N_c is more efficient and unbiased than N_c and Nc. The second question was put by Fuglsang in 2005 and unsolved. This thesis proves S plays a role of negative entropy, and discusses the derivation of the equivalence of S and H in segmenting DNA sequences. The two questions were put by C. T. Zhang in 2005.In the last chapter, based on the physics-chemical distances between amino acids and mutation frequencies between codons, a new scheme measuring codon volatility is proposed. Meanwhile, this thesis brings forth the advantage of new scheme in similarity analysis.