小RNA是一種長度小於200個核苷酸的RNA分子，其中微小RNA和小干擾RNA是兩種常見的小RNA。在植物中，這兩種小RNA已知是控制基因表現的重要調控因子，會誘導訊息RNA的降解。近年來，許多植物研究都利用次世代定序發掘小RNA的調控途徑，因此也開發了許多用於分析次世代定序資料的生物資訊工具。然而，大部分的方法都只具有分析小RNA的表現量或是預測新穎的微小RNA等功能，卻幾乎沒有辦法同時分析小RNA對下游調控基因所造成的影響。另一方面，目前還沒有工具能夠分析植物病毒和宿主之間交互作用的機制，也沒辦法分析兩個病毒共同感染所產生的協同機制。為了解決這些問題，本研究開發了一個完整的小RNA次世代定序資料分析系統 (Small RNA Illustration System，簡稱sRIS)。本系統具有兩個主要的分析程式套件，其中一個是用於分析小RNA的概況，不只能夠找出微小RNA，還能夠辨別病毒衍生的小干擾RNA。另一個則是用於預測小RNA的調控標的，此部分不僅透過生物資訊方法進行預測，同時整合降解組的定序資料來提高預測可信度。除此之外，本系統特別以圖表方式呈現分析結果，讓使用者能更輕易判讀分析數據。最後我們也利用一組蝴蝶蘭的小RNA次世代定序資料進行實例分析，透過本系統的分析，能快速找出在特定條件下重要的小RNA，並將之作為後續實驗的候選標的。本系統之開發，相信必能提升小RNA次世代定序資料分析的效率。目前sRIS系統可由以下網址免費取得: http://sris.itps.ncku.edu.tw/

Small RNA (sRNA) is RNA molecule that is shorter than 200 nt and has many different types. Both microRNA (miRNA) and short interfering RNA (siRNA) are well-known sRNAs to control gene expression based on degradation of target mRNA in plants. Recently, next-generation sequencing (NGS) has been broadly applied to reveal regulatory pathways of plant sRNA in many researches. Consequently, numerous bioinformatics tools have been developed for analyzing sRNA NGS data. However, most methods focus on the study of sRNA expression profiles or novel miRNAs prediction. The analysis of sRNA target genes is usually not integrated into their pipelines. On the other hand, none of them can be applied to identify the interaction mechanisms between host and virus, even though the synergism effects between two viruses. In order to solve the problems mentioned above, a comprehensive system, named as Small RNA Illustration System (sRIS), was developed for small RNA next-generation sequencing data analysis in this study. There are two major packages in this system. One of them is for sRNA overview analysis. It can not only identify miRNA but also investigate virus-derived small interfering RNA (vsiRNA). The other is for sRNA target prediction. Besides bioinformatics calculation, degradome sequencing data is used to enhance the evidence of target prediction. Moreover, the figures and tables of each analysis outputs can be retrieved from this system, and help users to realize the results more easily. Finally, a series of orchid sRNA sequencing data was used to perform the efficiency of the sRIS. Accordingly, several important sRNAs in a specific condition were rapidly identified as good candidates for further experiments validation. We believe this work is helpful to increase the effectiveness of sRNA NGS data analysis. Small RNA illustration system is freely available at: http://sris.itps.ncku.edu.tw/

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