The State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W22-8. doi: 10.1093/nar/gks554. Epub 2012 Jun 12.
Small RNAs (smRNAs) in plants, mainly microRNAs and small interfering RNAs, play important roles in both transcriptional and post-transcriptional gene regulation. The broad application of high-throughput sequencing technology has made routinely generation of bulk smRNA sequences in laboratories possible, thus has significantly increased the need for batch analysis tools. PsRobot is a web-based easy-to-use tool dedicated to the identification of smRNAs with stem-loop shaped precursors (such as microRNAs and short hairpin RNAs) and their target genes/transcripts. It performs fast analysis to identify smRNAs with stem-loop shaped precursors among batch input data and predicts their targets using a modified Smith-Waterman algorithm. PsRobot integrates the expression data of smRNAs in major plant smRNA biogenesis gene mutants and smRNA-associated protein complexes to give clues to the smRNA generation and functional processes. Besides improved specificity, the reliability of smRNA target prediction results can also be evaluated by mRNA cleavage (degradome) data. The cross species conservation statuses and the multiplicity of smRNA target sites are also provided. PsRobot is freely accessible at http://omicslab.genetics.ac.cn/psRobot/.
植物中的小 RNA（smRNAs），主要是 microRNAs 和 small interfering RNAs，在转录和转录后基因调控中发挥着重要作用。高通量测序技术的广泛应用使得实验室中批量生成 smRNA 序列成为可能，从而显著增加了对批量分析工具的需求。PsRobot 是一个基于网络的易于使用的工具，专门用于鉴定具有茎环结构前体（如 microRNAs 和短发夹 RNA）的 smRNAs 及其靶基因/转录本。它执行快速分析，以识别批量输入数据中具有茎环结构前体的 smRNAs，并使用改进的 Smith-Waterman 算法预测它们的靶标。PsRobot 整合了主要植物 smRNA 生物发生基因突变体和 smRNA 相关蛋白复合物中的 smRNAs 表达数据，为 smRNA 生成和功能过程提供线索。除了提高特异性外，还可以通过 mRNA 切割（降解组）数据评估 smRNA 靶标预测结果的可靠性。还提供了 smRNA 靶标位点的跨物种保守状态和多重性。PsRobot 可在 http://omicslab.genetics.ac.cn/psRobot/ 免费访问。
