SoMART: a web server for plant miRNA, tasiRNA and target gene analysis
SoMART: a web server for plant miRNA, tasiRNA and target gene analysis
复制标题
DOI：
10.1111/j.1365-313x.2012.04922.x
复制
发表时间：
2012-06-01
期刊：
影响因子：
7.2
通讯作者：
Baker, Barbara
中科院分区：
文献类型：
--
作者：
Li, Feng;Orban, Ryan;Baker, Barbara
植物microRNAs （miRNAs）和反式小干扰rna （tasiRNAs）在多种生物过程中发挥着重要作用。生物信息学预测和小RNA （sRNA）克隆是鉴定mirna和tasirna及其靶标的最重要方法。然而，这些方法并不是每个研究人员都能轻易使用的。在这里，我们介绍了SoMART，一个miRNA/tasiRNA分析资源和工具的web服务器，它是为那些对鉴定miRNA或tasiRNA有兴趣的研究人员设计的，这些miRNA或tasiRNA可能调节感兴趣的基因。该服务器包括四套工具：用于检测靶向输入基因的sRNAs的切片器检测器，用于检测源自输入基因的降解(d)RNA产物的dRNA映射器，用于识别输入sRNAs的miRNA前体（MIRs）或tasiRNA前体（TASs）的PreMIR检测器，以及用于将sRNAs映射到输入基因上的sRNA映射器。我们还开发了一种rna -seq协议，以实现更长的dRNA读取，以便通过dRNA制图器更好地表征miRNA前体。为了验证服务器功能和稳健性，我们安装了sRNA、dRNA并收集了拟南芥和茄属植物的基因组DNA或转录组数据库，并在马铃薯（Solanum tuberosum）中鉴定了mir172介导的APETALA2基因调控，并在番茄（Solanum lycopersicum）中证实了mir390触发的TAS3基因的保守性。更重要的是，我们预测了mir482触发的TAS5在番茄中的存在。通过对拟南芥中21个已验证的miRNA靶点和115个miRNA前体的分析，进一步验证了该服务器的效率和准确性。SoMART可在。
Plant microRNAs (miRNAs) and trans-acting small interfering RNAs (tasiRNAs) play important roles in a variety of biological processes. Bioinformatics prediction and small RNA (sRNA) cloning are the most important approaches for identification of miRNAs and tasiRNAs and their targets. However, these approaches are not readily accessible to every researcher. Here we present SoMART, a web server for miRNA/tasiRNA analysis resources and tools, which is designed for researchers who are interested in identifying miRNAs or tasiRNAs that potentially regulate genes of interest. The server includes four sets of tools: Slicer detector for detecting sRNAs targeting input genes, dRNA mapper for detecting degradome (d)RNA products derived from input genes, PreMIR detector for identifying miRNA precursors (MIRs) or tasiRNA precursor (TASs) of input sRNAs, and sRNA mapper for mapping sRNAs onto input genes. We also developed a dRNA-seq protocol to achieve longer dRNA reads for better characterization of miRNA precursors by dRNA mapper. To validate the server function and robustness, we installed sRNA, dRNA and collected genomic DNA or transcriptome databases from Arabidopsis and solanaceous plants, and characterized miR172-mediated regulation of the APETALA2 gene in potato (Solanum tuberosum) and demonstrated conservation of MIR390-triggered TAS3 in tomato (Solanum lycopersicum). More importantly, we predicted the existence of MIR482-triggered TAS5 in tomato. We further tested and confirmed the efficiency and accuracy of the server by analyses of 21 validated miRNA targets and 115 miRNA precursors in Arabidopsis thaliana. SoMART is available at .