The Research On Graphical Representation Of RNA Secondary Structure And Analysis Of Similarity Based On The Characteristics Of Arc

With the completion of HGP (Human Genome Project) and the implementation ofthe genome projects of some models, people’s enthusiasm on the biological sequencesand gene research has been further increasing, as a result, it has brought about largesequence databases and structure databases. How to scientifically analyze and processthese datas and find the rule to instruct the biologic research and experiment is themain task of present bioinformatics. How to propose an effective graphicrepresentation of gene sequences and make an analysis among these Graphics-basedsequences, particularly for the sequences containing pseudoknot structures is one ofthe hot topics of biological information.Graphical representation of biological sequences is a powerful and visual toolwhich is developing and being applied to RNA secondary structure analysis. It candiscover the biological information which is hidden in RNA sequences related tostructures and functions. The pseudoknot structure is an important constituent of theRNA sequence, which has a major impact on the RNA sequence function, and manyimportant functions are located in the pseudoknot region. Based on the analysis of thecurrent graphical representations involving2-dimensional,3-dimensional andhigher-dimensional representations, this thesis proposes a new graphicalrepresentation of RNA secondary structure, reduces the syntax of the existingrewriting rules of arc graph grammar, poses a calculation of the characteristics of thearc of RNA secondary structure with pseudoknot, and gets a graphical representationof RNA secondary structure which is based on the characteristics of the arc. The mainachievements are summarized as below:First, in view of the chemical properties and structure features of RNA secondarystructure and the differences between before and after base pairs, this thesis proposesa new2D graphical representation of the RNA secondary structure——set of V curve,and proves the non-degradation function of it and achieves the visualization of thegene sequence data. Then the set of V curve is applied to the end of secondarystructure of nine RNA-3viruses and the numerical features of these RNA secondarysutructures are given and the similarities among them are analyzed,Second, the existing rewriting rules of arc graph grammar are shortened, asingle-arc rewriting method is redefined, and the RNA secondary structure with pseudoknot order rewriting is realized, then the infinite number of RNA secondarystructure arc graphs are mapped to a limited number of rewriting rules, the calculationmethods and formulas of arc characteristics based on the great closed interval areproposed to divide the interval of RNA secondary structure, the arc characteristicsbased on the great closed interval is applied to the graphical representation of RNAsecondary structure with pseudoknot as a parameter,proposed a new2D graphicalrepresentation——set of P curve,which can express RNA secondary structure withpseudoknot, and it is also non-degradation. Finally the method is applied the graphicalrepresentation to fourteen RNA secondary structures, getting the digital features ofRNA secondary structure with pseudoknot based on the graphical representation, theresults of similarity analysis show that the method is feasible.