Development Of A Platform For Alternative Polyadenylation Analysis And Visualization

Poly(A) refers to the covalent link between polyadenylation and messenger RNA (mRNA). Poly(A) tail is added to the adenosine chain of mRNA in a template-free way, which is an important structure feature of eukaryotes mRNA and has important implications for gene expression regulation in Eukaryota. Numerous studies have shown that alternative polyadenylation(APA) sites widely exist in eukaryotic mRNA and they play an important role in regulating the stage of gene expression. The study of different types of poly(A) sites and its differential expression will be conducive to deep understanding of gene expression regulation, promote the research of molecular, biological evolutionary mechanisms in the polyadenylation process of eukaryotic mRNA.High-throughput analysis of large-scale sequence data is a significant means on the search of plant polyadenylation and the comparative analysis of poly(A) sites is the key to explore biological gene expression in plants. With the development of DNA sequencing technology, conventional sequencing experiment can produce millions of sequencing data. Biologists are able to obtain unprecedented amount of poly(A) site data from different conditions. It is in urgent need to develop a user friendly tool to visualize the massive poly(A) site data to assist biologists for further APA analysis. However, there are not a specific platform for the study of APA and can not be used to visualize poly(A) sites of genes.To meet the above demand, this paper developed a set of visualized online Web platform for the analysis of APA. The main interface is based on Linux, Apache, MySQL and PHP, providing interface entrance, operating instruction and data upload service for analysis and visualization platform. The analysis and visualization platform was developed based on Smart GWT (Google Web Toolkit) with Java language. It integrates MySQL, Spring, Hibernate, and MVP (Model-View-Presenter) design pattern. The platform uses the data of various tissues in arabidopsis and rice root tissue as input and synthetically analyze the poly(A) sites distribution of a variety conditions as well as APA tissue-specific and species-specific, objective To improve the efficiency of biological experiment and data analysis. This platform would have contributed to the development of the plant sites and recognition research.