Mathematical Modeling And Analyst Of F/10 And G/11 Xylanase Family

The similarity research of gene sequence is one of the most hot question in the area of bioinformatics. With the completion of human genome project, a large number of gene sequences are measured, similarity research of protein sequences become more complex and workload more heavy. Therefore, the study of new methods of sequence alignment has become a urgent issue. In fact, graphical representation method of gene sequences is an effective method of research sequence similarity. The mains contents are listed as follows:1,Based on the chaos game representation method (CGR) of DNA sequences and 4 Line Graphical Representation method (4-LGR) of DNA sequences, we proposed a novel graphical representation method of DNA sequences—Matrix Graphical Representation (MGR).Further, on the basis of the above three kinds of DNA sequences model, we extend graphical representation of protein sequences based on the detailed HP model respectively. Then, the similarity of protein sequences is compared.2,Based on the detailed HP model, using the idea of matrix graphical represention of protein (MGR) and numerical description, we proposed a new method to align two protein sequences. Through review numerical description graph of protein sequences and compute Euclidean distance d between that two sequences, we analyse the similarity of protein sequences about two xylnase family.3,According to the work of Shi Xiufan and Zhu Ping et al, the paper computes the relative usage degree of the synonymous codon of F/10 and G/11 Xylanase: (RSCU and QRSCU). Through the analysis and comparison we can see that based on the classification of the quasi-amino acid can more abvious show the consistent preference to the synonymous codon. That is to say, based on the classification of quasi-amino acids, F/10 and G/11 Xylanase prefer to use the codons with strong combination of the codon-anticodon, just the codons ending with g/c. The conclusion accords with the preference studying about the 78 human genes. And further verified codon preference closely related to quasi-amino acids coding method.4,According to the CGR of the DNA sequences proposed by Jeffrey in 1990, the paper researched the gene sequences of F/10 and G/11 family and gived the CGR of gene sequences. At the same time, we further gived the corresponding probability matrix for the second-order Markov Chain model and computed the relative usage degree of the synonymous codon. Through the analyst we can see that the use of preferences of the synonymous codon closely related to the G/C content and molecular evolution. The paper's results indicate that the research is meaningful, and it has great practical value for future research in this area.