psRNATarget: a plant small RNA target analysis server.
psRNATarget: a plant small RNA target analysis server.
复制标题
DOI：
10.1093/nar/gkr319
复制
发表时间：
2011-07
影响因子：
14.9
通讯作者：
Zhao PX
中科院分区：
文献类型：
--
作者：
Dai X;Zhao PX
植物内源性非编码小RNA（20-24 nt），包括microRNA（miRNAs）和小干扰RNA（ta-siRNAs），在基因表达调控网络（GRNs）中起着重要作用。例如，许多转录因子和发育相关基因已被报道为这些调控小RNA的靶点。虽然已经开发了许多miRNA靶标预测算法和程序，但大多数都是针对动物miRNA设计的，这些动物miRNA在靶标识别过程中与植物miRNA显著不同。这些差异需要开发单独的植物miRNA（和ta-siRNA）靶标分析工具。我们提出psRNATarget，一个植物小RNA目标分析服务器，它具有两个重要的分析功能：（i）小RNA和目标转录本之间的反向互补匹配使用一个成熟的评分模式，和（ii）通过计算所需的未配对能量（UPE）靶位点的可及性评估“打开”mRNA上的小RNA的靶位点周围的二级结构。psRNATtarget结合了植物miRNA靶标识别的最新发现，例如，它区分了翻译和转录后抑制，并且它报告了可能影响小RNA与靶转录物结合活性的小RNA/靶位点对的数量。psRNATtarget服务器设计用于对下一代数据进行高吞吐量分析，并具有在Linux群集上运行的高效分布式计算后端管道。服务器前端集成了三个简化的用户友好界面，以接受用户提交或预加载的小RNA和转录本序列;并输出小RNA/靶对的全面列表，以及用于批量下载、关键字搜索和结果排序的在线工具沿着。psRNATarget服务器可在http://plantgrn.noble.org/psRNATarget/上免费获得。
Plant endogenous non-coding short small RNAs (20–24 nt), including microRNAs (miRNAs) and a subset of small interfering RNAs (ta-siRNAs), play important role in gene expression regulatory networks (GRNs). For example, many transcription factors and development-related genes have been reported as targets of these regulatory small RNAs. Although a number of miRNA target prediction algorithms and programs have been developed, most of them were designed for animal miRNAs which are significantly different from plant miRNAs in the target recognition process. These differences demand the development of separate plant miRNA (and ta-siRNA) target analysis tool(s). We present psRNATarget, a plant small RNA target analysis server, which features two important analysis functions: (i) reverse complementary matching between small RNA and target transcript using a proven scoring schema, and (ii) target-site accessibility evaluation by calculating unpaired energy (UPE) required to ‘open’ secondary structure around small RNA’s target site on mRNA. The psRNATarget incorporates recent discoveries in plant miRNA target recognition, e.g. it distinguishes translational and post-transcriptional inhibition, and it reports the number of small RNA/target site pairs that may affect small RNA binding activity to target transcript. The psRNATarget server is designed for high-throughput analysis of next-generation data with an efficient distributed computing back-end pipeline that runs on a Linux cluster. The server front-end integrates three simplified user-friendly interfaces to accept user-submitted or preloaded small RNAs and transcript sequences; and outputs a comprehensive list of small RNA/target pairs along with the online tools for batch downloading, key word searching and results sorting. The psRNATarget server is freely available at http://plantgrn.noble.org/psRNATarget/.
登录
查看更多内容
通过对简短阅读的深度测序发现大麦miRNA。
影响因子：
4.4
作者：
Schreiber AW;Shi BJ;Huang CY;Langridge P;Baumann U
通讯作者：
Baumann U
影响因子：
3.5
作者：
Xie, Fu Liang;Huang, Si Qi;Yang, Zhi Min
通讯作者：
Yang, Zhi Min
影响因子：
11.6
作者：
Howell, Miya D.;Fahlgren, Noah;Carrington, James C.
通讯作者：
Carrington, James C.
影响因子：
16
作者：
Jones-Rhoades, MW;Bartel, DP
通讯作者：
Bartel, DP
影响因子：
4.4
作者：
Ruan, Meng-Bin;Zhao, Ying-Tao;Yang, Wei-Cai
通讯作者：
Yang, Wei-Cai