Research On The Prediction Algorithm Of RNA Folding Structure Based On Basin Jump Diagram With False Knots

Ribonucleic Acid(RNA)as a kind of biological macromolecules plays an important role in connecting DNA with protein in the process of gene expression.It has significant impact on gene expression,gene transformation and so on.By some biological experiments,we have already found many RNA primary structures.Measured by X-ray crystallography amd NMR,we also have found tertiary structure of RNA.It is an important vehicle for RNA structure prediction using computer and mathematical modeling,on the one hand,it is very hard to predict using physical experiment,on the other hand,it cannot deal with a mass of sequences data only relying on the physics experiment.There is a class of substructure called pseudoknots formed by stem nesting and crossing.The pseudoknots of RNA play a key role in many kinds of RNA catalysis,so recently researchers pay more attention to it.After hard working of so many researchers,some mature predicting methods of RNA secondary structure were proposed,which each of them has their own advantages and disadvantages.We have done in-depth research on RNA secondary structure under these circumstances,and we also have studied the prediction algorithm of RNA folding structure with pseudoknots based on basin hopping graph and barrier tree.By calculating the minimum free energy of RNA secondary structure containing pseudoknots,an improved algorithm was proposed to constructe barrier tree.It has shown that the improved algorithm is available and effective.The main work of the paper is as follows:1.To analyze the effect of pseudoknot on RNA folding structure,it is proposed to construct BHG by calculating the minimum free energy.It is calculated that the four hypothetical types,which can be converted by increasing or decreasing base pairs under the BHG framework.The Gfold software was used for differential expression gene analysis in RNA-seq data,we can deep understand RNA folding structures,the experiment results indicate it is fine.2.By calculating the composition ratio of the local minimum energy in the lower part of the RNA molecule,with and without the pseudo-junction.We analyze the contribution of the pseudoknots in the local minimum energy during the RNA folding process.