Rennie William, Kanoria Shaveta, Liu Chaochun, Carmack C Steven, Lu Jun, Ding Ye
New York State Department of Health, Wadsworth Center, Center for Medical Science, Albany, NY, USA.
Department of Genetics, Yale Stem Cell Center, Yale University, New Haven, CT, USA.
Methods Mol Biol. 2019;1970:31-42. doi: 10.1007/978-1-4939-9207-2_3.
Computational prediction of miRNA binding sites on target mRNAs facilitates experimental investigation of miRNA functions. In this chapter, we describe STarMir and STarMirDB, two application modules of the Sfold RNA package. STarMir is a Web server for performing miRNA binding site predictions for mRNA and target sequences submitted by users. STarMirDB is a database of precomputed transcriptome-scale predictions. Both STarMir and STarMirDB provide comprehensive sequence, thermodynamic, and target structure features, a logistic probability as a measure of confidence for each predicted site, and a publication-quality diagram of the predicted miRNA-target hybrid. In addition, STarMir now offers a new quantitative score to address combined regulatory effects of multiple seed and seedless sites. This score provides a quantitative measure of the overall regulatory effects of both seed and seedless sites on the target. STarMir and STarMirDB are freely available to all through the Sfold Web application server at http://sfold.wadsworth.org .
计算预测靶标mRNA上的miRNA结合位点有助于对miRNA功能进行实验研究。在本章中，我们将介绍Sfold RNA软件包的两个应用模块STarMir和STarMirDB。STarMir是一个网络服务器，用于对用户提交的mRNA和靶标序列进行miRNA结合位点预测。STarMirDB是一个预先计算的转录组规模预测的数据库。STarMir和STarMirDB都提供了全面的序列、热力学和靶标结构特征，一个逻辑概率作为每个预测位点可信度的度量，以及预测的miRNA-靶标杂交体的高质量发表图表。此外，STarMir现在提供了一个新的定量评分，以解决多个种子和无种子位点的联合调控效应。该评分提供了种子和无种子位点对靶标的总体调控效应的定量度量。通过http://sfold.wadsworth.org的Sfold网络应用服务器，所有人都可以免费使用STarMir和STarMirDB。
