The Establishment Of The MicroRNA Computational Analysis Platform

This paper presents an establishment of a microRNA computational analysis platform, which includes microRNA prediction tools that mining new microRNA from high-throughput data, microRNA target prediction tools and ta-siRNA analysis tool.As a research focus in recent years, microRNAs are a class of small non-coding RNAs, it binds the3’-UTR of mRNAs by specific binding and inhibition of its expression. This class of small RNA molecular is involved in almost all cellular processes in living organisms, and shows regulatory functions in a variety of species, and microRNA has attracted more and more attention cause its powerful biological function.With the rapid development and universal application of RNA-seq technology, a large number of RNA data has been accumulated, and such data is still increasing. Developing effective computational tools to discover biological knowledge from this data is an important task of bioinformatics. The RNA-seq data contain many known microRNA sequence and other types of functional RNA sequence such as tRNA, rRNA, etc. Likewise, the RNA-seq data also contain a large number of unknown microRNA. In this study, the characteristics of the microRNA biosynthesis is been used in the prediction of microRNA from the RNA-seq data.To further study the role of microRNA in vivo, we need to study the genes the regulated by microRNA. MicroRNA silence the target gene by binding to its3UTR. We designed a set of algorithm which is based on the way that microRNA plays its role in vivo to predict the target of microRNA. In this process, we take into account the energy of the secondary structure formed by microRNA sequence with its predicted target sequence, and their sequence similarity.Trans-acting RNA (ta-siRNA) which is generated by microRNA-mediated mRNA degradation is a kind of small interfering RNA found in plant cells. Ta-siRNA play a role in plant cell by a microRNA-like way, they all silence the target gene by binding to the3’UTR of the target gene. Researches about the generating of ta-siRNA and ta-siRNA participated pathway are meaningful to the understanding of the regulatory mechanism of microRNA.