A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer).
A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer).
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DOI：
10.1186/s12859-016-1071-0
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发表时间：
2016-05-17
影响因子：
3
通讯作者：
Gregory BD
中科院分区：
文献类型：
--
作者：
Berkowitz ND;Silverman IM;Childress DM;Kazan H;Wang LS;Gregory BD
RNA 分子在核苷酸之间氢键模式的引导下折叠成复杂的三维形状。这种碱基配对模式（称为 RNA 二级结构）对其细胞功能至关重要。最近开发了几种不同的方法，利用高通量测序在转录组范围内测定 RNA 二级结构。每种方法都有自己的优点和注意事项，但是没有广泛可用的工具来可视化和比较这些不同方法的结果。为了解决这个问题，我们开发了 Structure Surfer，这是一种数据库和可视化工具，用于检查来自人类和小鼠的六个转录组范围数据集中的 RNA 二级结构 (http://tesla.pcbi.upenn.edu/strucuturesurfer/)。数据集是使用四种不同的基于高通量测序的方法生成的。每一项都使用特定于其实验设计的评分流程进行分析。 Structure Surfer 的用户能够查询各个位点并检测多个站点的趋势。在这里，我们描述了包含的数据集及其差异。我们通过检查已知的结构元素来说明数据库的功能，并探索使用组合数据来检测结构趋势的示例用例。总的来说，Structure Surfer 提供了一个易于使用的数据库和可视化界面，允许用户查询当前可用的哺乳动物转录组范围的 RNA 二级结构信息。本文的在线版本 (doi:10.1186/s12859-016-1071-0) 包含补充材料，可供授权用户使用。
RNA molecules fold into complex three-dimensional shapes, guided by the pattern of hydrogen bonding between nucleotides. This pattern of base pairing, known as RNA secondary structure, is critical to their cellular function. Recently several diverse methods have been developed to assay RNA secondary structure on a transcriptome-wide scale using high-throughput sequencing. Each approach has its own strengths and caveats, however there is no widely available tool for visualizing and comparing the results from these varied methods. To address this, we have developed Structure Surfer, a database and visualization tool for inspecting RNA secondary structure in six transcriptome-wide data sets from human and mouse (http://tesla.pcbi.upenn.edu/strucuturesurfer/). The data sets were generated using four different high-throughput sequencing based methods. Each one was analyzed with a scoring pipeline specific to its experimental design. Users of Structure Surfer have the ability to query individual loci as well as detect trends across multiple sites. Here, we describe the included data sets and their differences. We illustrate the database’s function by examining known structural elements and we explore example use cases in which combined data is used to detect structural trends. In total, Structure Surfer provides an easy-to-use database and visualization interface for allowing users to interrogate the currently available transcriptome-wide RNA secondary structure information for mammals. The online version of this article (doi:10.1186/s12859-016-1071-0) contains supplementary material, which is available to authorized users.