Plant small molecule RNA mainly includes microRNA and small interfering RNA, which plays an important role in the transcription and post-transcriptional regulation of genes. The gradual maturity and wide application of second-generation sequencing technology has greatly promoted the development of small molecule RNA related research. In-depth sequencing of small molecule RNA in different tissues and materials has become a routine method for studying small molecule RNA. Therefore, bioinformatics analysis of these data has become an increasingly prominent problem facing researchers.
Researchers in the research group of Wang Xiujie of the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences have developed an online small molecule RNA integration analysis software psRobot. The software only needs the user to submit the mature body sequence of small molecule RNA, and can use a variety of pre-stored high-throughput data systems to identify whether these small molecule RNAs are microRNAs (or small RNAs with hairpin structure precursors) and their Target gene situation. The online tool is mainly divided into two functional modules. The first functional module provides information related to the small molecule RNA itself, including the positioning of the small molecule RNA in the reference genome and the position of the stem-loop structure, and the synthesis of proteins in different small molecule RNA The expression level in mutant or AGO binding experiments. Users can judge the production and action process of small molecule RNA based on the above analysis results. The second functional module performs target gene prediction of small-molecule RNA, and provides biological experiment data information including the list of all target gene sites in the reference sequence library, the multiplicity of target sites, the conservation of target sites, and degradation group data. . Through the above tools, users can easily obtain the analysis of the production process, mechanism of action and biological functions of the analyzed small molecule RNA, which provides great convenience for the systematic study of the function of small molecule RNA. The website of PsRobot is: http://omicslab.genetics.ac.cn/psRobot/.
The research was published online in the British bioinformatics journal Nucleic Acids Research (DOI: 10.1093 / nar / gks554). Wu Huajun and Ma Yingke, PhD students of Wang Xiujie's research group, are the co-first authors of the paper.
The research was funded by the National Natural Science Foundation of China, the Chinese Academy of Sciences and the Ministry of Agriculture.
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