State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Beijing 10091, China.
Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
Brief Bioinform. 2021 Jan 18;22(1):463-473. doi: 10.1093/bib/bbz151.
Small noncoding RNAs (sRNA/sncRNAs) are generated from different genomic loci and play important roles in biological processes, such as cell proliferation and the regulation of gene expression. Next-generation sequencing (NGS) has provided an unprecedented opportunity to discover and quantify diverse kinds of sncRNA, such as tRFs (tRNA-derived small RNA fragments), phasiRNAs (phased, secondary, small-interfering RNAs), Piwi-interacting RNA (piRNAs) and plant-specific 24-nt short interfering RNAs (siRNAs). However, currently available web-based tools do not provide approaches to comprehensively analyze all of these diverse sncRNAs. This study presents a novel integrated platform, sRNAtools (https://bioinformatics.caf.ac.cn/sRNAtools), that can be used in conjunction with high-throughput sequencing to identify and functionally annotate sncRNAs, including profiling microRNAss, piRNAs, tRNAs, small nuclear RNAs, small nucleolar RNAs and rRNAs and discovering isomiRs, tRFs, phasiRNAs and plant-specific 24-nt siRNAs for up to 21 model organisms. Different modules, including single case, batch case, group case and target case, are developed to provide users with flexible ways of studying sncRNA. In addition, sRNAtools supports different ways of uploading small RNA sequencing data in a very interactive queue system, while local versions based on the program package/Docker/virtureBox are also available. We believe that sRNAtools will greatly benefit the scientific community as an integrated tool for studying sncRNAs.
小非编码 RNA（sRNA/sncRNAs）来源于不同的基因组位置，在细胞增殖和基因表达调控等生物学过程中发挥重要作用。下一代测序（NGS）为发现和定量各种 sncRNA 提供了前所未有的机会，例如 tRFs（tRNA 衍生的小 RNA 片段）、phasiRNAs（相化、二级、小干扰 RNA）、Piwi 相互作用 RNA（piRNAs）和植物特异性 24nt 短干扰 RNA（siRNAs）。然而，目前可用的基于网络的工具并没有提供全面分析所有这些不同 sncRNA 的方法。本研究提出了一个新的综合平台 sRNAtools（https://bioinformatics.caf.ac.cn/sRNAtools），它可以与高通量测序结合使用，用于鉴定和功能注释 sncRNA，包括 miRNA、piRNA、tRNA、small nuclear RNA、small nucleolar RNA 和 rRNA 的分析，以及 21 种模式生物的 isomiR、tRF、phasiRNA 和植物特异性 24nt siRNA 的发现。不同的模块，包括单个案例、批量案例、组案例和目标案例，被开发出来，为用户提供了灵活的 sncRNA 研究方式。此外，sRNAtools 支持以非常交互的队列系统上传小 RNA 测序数据的不同方式，同时也提供基于程序包/Docker/virtureBox 的本地版本。我们相信，sRNAtools 将作为研究 sncRNA 的综合工具，极大地造福科学界。
