RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data.
RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data.
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DOI：
10.1093/nar/gkw362
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发表时间：
2016-07-08
影响因子：
14.9
通讯作者：
Lu ZJ
中科院分区：
文献类型：
--
作者：
Wu Y;Qu R;Huang Y;Shi B;Liu M;Li Y;Lu ZJ
几种高通量技术已被开发用于在多个物种的转录组水平上探测 RNA 碱基对和环。然而，为了获得最终的RNA二级结构，需要大量的努力和大量的专业知识来统计处理探测数据并将其与自由能模型相结合。因此，我们开发了一个通过实验数据增强的RNA二级结构预测服务器（RNAex）。 RNAex 是一个网络界面，使非专业人士能够轻松访问尖端结构探测数据并预测体内和体外数据增强的 RNA 二级结构。 RNAex 注释了预测结构上的 RNA 编辑、RNA 修饰和 SNP 位点。它提供了四种结构折叠方法，即约束式MaxExpect、SeqFold、RNAstruct（Fold）和RNAfold，可供用户选择。这四种折叠方法的性能已通过先前出版物对已知结构的验证。我们将探测实验的原始测序数据重新映射到每个物种的整个基因组。因此，RNAex 使用户能够预测人类、小鼠、酵母和拟南芥中已知和新型 RNA 转录本的二级结构。 RNAex Web 服务器位于 http://RNAex.ncrnalab.org/。
Several high-throughput technologies have been developed to probe RNA base pairs and loops at the transcriptome level in multiple species. However, to obtain the final RNA secondary structure, extensive effort and considerable expertise is required to statistically process the probing data and combine them with free energy models. Therefore, we developed an RNA secondary structure prediction server that is enhanced by experimental data (RNAex). RNAex is a web interface that enables non-specialists to easily access cutting-edge structure-probing data and predict RNA secondary structures enhanced by in vivo and in vitro data. RNAex annotates the RNA editing, RNA modification and SNP sites on the predicted structures. It provides four structure-folding methods, restrained MaxExpect, SeqFold, RNAstructure (Fold) and RNAfold that can be selected by the user. The performance of these four folding methods has been verified by previous publications on known structures. We re-mapped the raw sequencing data of the probing experiments to the whole genome for each species. RNAex thus enables users to predict secondary structures for both known and novel RNA transcripts in human, mouse, yeast and Arabidopsis. The RNAex web server is available at http://RNAex.ncrnalab.org/.