Research And Implementation Of The Prediction Method Of Long Non-coding RNA Secondary Structure

In the recent years,long non-coding RNAs(IncRNAs)have been attracted much attention due to their potential biological functions.With the assistance of high-throughput transcriptome sequencing technology(RNA-Seq),researchers have discovered hundreds of thousands of lncRNAs in a variety of organisms including mammals,such as humans and mice.Studies have shown that lncRNAs are generally characterized by low sequence conservation and low expression level,making it difficult to establish a direct link between sequence and function.Given that functional non-coding RNAs(ncRNAs)are conserved at the secondary structure level,it is concluded that the secondary structure of functionally similar lncRNAs is also somewhat conservative.This thesis focuses on the research and development of the secondary structure prediction of lncRNAs based on bioinformatic methods.The main work is as follows:(1)The mainstream methods of RNA secondary structure prediction(mainly included sequence comparison method,dynamic programming algorithm,and classification prediction method based on machine learning)were analyzed,and the advantages and disadvantages of these methods were analyzed and compared.Then the main ncRNA sequence and structure databases were reviewed,including miRBase,GtRNAdb,RNase P database,Rfam,GENCODE,lncRNAdb,and NONCODE.(2)Base on the above,an evaluation system for RNA secondary structure prediction(lncRScan-Fold-Assess)has been proposed.Its main functions include:reporting of RNA secondary structure information predicted,calculatoffing prediction accuracy of the RNA secondary structure predicted,and conducting comparison among different RNA secondary structure prediction methods.LncRScan-Fold-Assess provides predictive functions for RNA secondary structure prediction using RNAfold,MARNA,Mfold,Pfold,Sfold,RNAstructure,and CentroidFold.(3)In order to apply our evaluation system for RNA secondary structure prediction to scientific research.In the experiment,IncRScan-Fold-Assess was applied to miRNA,tRNA,RNase P RNA,ncRNA.and lncRNA.The results showed that when conducting prediction for a group of homologous sequences,the Pfold and centroid method CentidixFold based on comparative analysis were significantly better than RNAfold,mfold,Sfold,and RNAStructure based on the minimal free energy.When predicting a single sequence,there is no significant difference in the results obtained by different prediction methods.In summary,users can use IncRScan-Fold-Assess to evaluate the performance of multiple RNA secondary structure prediction methods simultaneously,and can select a better method according to the output results.LncRScan-Fold-Assess can help to improve the efficiency of current IncRNA secondary structural prediction.