Development Of Reproductive Biology Related Bioinformatics Tools And Databases

In this article, I summarized the work done on bioinformatics in the field of reproductive biology within the past few years. Among all the known small RNAs, miRNA is the most important and well researched. Thus, the research approach and techniques on it is the most abundant. MiRNAs are expressed with special and temporal specificities and function either by degrading its target mRNA or by inhibiting their translations, which subsequently influence the development and pathogenesis of animals. Despite of the important roles of miRNAs, it is always energy consuming to find novel miRNAs and their targets. This, together with the difficulty in relating molecular experiment, would largely restrain the research progress in relating areas. A commonly used method to solve this problem is to do analysis through computational biology before doing experiments, which would greatly reduce the number of candidate novel miRNAs and their targets, and consequently help the progression of following experiments in vitro and in vivo.With the development of high-throughput sequencing technology, the second generation sequencing is widely used in the quantitative analysis of samples of small and medium-sized RNA. However, few directions can be provided just by getting the information on the expression of small RNA, especially miRNA. What the researchers in related areas need is a analysis platform online with a convenient operation interface, which may provide target prediction for miRNAs as well as GO analysis, pathway analysis and analysis on protein-protein interactions based on the sequencing data uploaded through website and the parameters set by the users. Finally, this online platform will not only show the enriched pathway and GO results to the customers, but also make predictions to the pathways through which the miRNAs regulate the animal or disease progress researched.It is also necessary to build a professional database to collect reported functional proteins for assortment, annotation and systematic analysis in the field of reproductive biology. Make predictions to the potential functions of unknown genes according to the protein and gene microarray information on gene expression in the database. Do further sorting and annotation to the predicted positive genes and integrate them into the knowledge database. This kind of professional database is of significance for summarizing current research outcomes and directing future experiments.We have now built tools or databases pinpoint the problems mentioned above. For example, we have developed online tools like miRD and SMESE for the prediction of novel miRNA and their targets. We have also developed online analyzing platform CPSS to analyze the second generation sequencing data. We have even developed two knowledge databases, FollADD and SpermatogenesisOnline, to solve problems in female and male reproduction respectively.