Wadsworth Center, New York State Department of Health, Center for Medical Science, 150 New Scotland Avenue, Albany, NY 12208, USA.
Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W114-8. doi: 10.1093/nar/gku376. Epub 2014 May 6.
STarMir web server predicts microRNA (miRNA) binding sites on a target ribonucleic acid (RNA). STarMir is an implementation of logistic prediction models developed with miRNA binding data from crosslinking immunoprecipitation (CLIP) studies (Liu,C., Mallick, B., Long, D., Rennie, W.A., Wolenc, A., Carmack, C.S. and Ding, Y. (2013). CLIP-based prediction of mammalian microRNA binding sites. Nucleic Acids Res., 41(14), e138). In both intra-dataset and inter-dataset validations, the models showed major improvements over established algorithms in predictions of both seed and seedless sites. General applicability of the models was indicated by good performance in cross-species validations. The input data for STarMir is processed by the web server to perform prediction of miRNA binding sites, compute comprehensive sequence, thermodynamic and target structure features and a logistic probability as a measure of confidence for each predicted site. For each of seed and seedless sites and for all three regions of a mRNA (3' UTR, CDS and 5' UTR), STarMir output includes the computed binding site features, the logistic probability and a publication-quality diagram of the predicted miRNA:target hybrid. The prediction results are available through both an interactive viewer and downloadable text files. As an application module of the Sfold RNA package (http://sfold.wadsworth.org), STarMir is freely available to all at http://sfold.wadsworth.org/starmir.html.
STarMir 网络服务器可预测靶 RNA 上的 microRNA（miRNA）结合位点。STarMir 是基于 miRNA 结合数据的逻辑预测模型的实现，这些数据来自交联免疫沉淀（CLIP）研究（Liu,C., Mallick, B., Long, D., Rennie, W.A., Wolenc, A., Carmack, C.S. and Ding, Y. (2013). CLIP-based prediction of mammalian microRNA binding sites. Nucleic Acids Res., 41(14), e138）。在数据集内和数据集间验证中，与既定算法相比，这些模型在种子和无种子位点的预测方面均显示出主要改进。模型在跨物种验证中的良好性能表明了其广泛适用性。STarMir 的输入数据由网络服务器处理，以执行 miRNA 结合位点预测、计算全面的序列、热力学和靶结构特征以及作为预测位点置信度的逻辑概率。对于种子和无种子位点以及 mRNA 的三个区域（3'UTR、CDS 和 5'UTR）中的每一个，STarMir 输出均包括计算的结合位点特征、逻辑概率以及预测 miRNA:靶杂交的出版物质量图。预测结果可通过交互式查看器和可下载的文本文件获得。作为 Sfold RNA 包（http://sfold.wadsworth.org）的应用模块，STarMir 免费提供给所有人，网址为 http://sfold.wadsworth.org/starmir.html。
