FoldAtlas: a repository for genome-wide RNA structure probing data.
FoldAtlas: a repository for genome-wide RNA structure probing data.
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Foldatlas：全基因组RNA结构探测数据的存储库。
DOI：
10.1093/bioinformatics/btw611
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发表时间：
2017-01-15
期刊：
影响因子：
--
通讯作者：
Ding Y
中科院分区：
文献类型：
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作者：
Norris M;Kwok CK;Cheema J;Hartley M;Morris RJ;Aviran S;Ding Y
大多数RNA分子形成内部碱基对，导致折叠的二级结构。这些结构中的一些已经被证明具有重要的功能。高通量的RNA结构化学探测方法产生数百万个测序读数，为RNA二级结构预测提供结构约束。目前，在没有计算专业知识的情况下，很难获得这些实验的处理数据。在这里，我们介绍FoldAtlas，这是一个用于访问数千份成绩单上的原始和经过处理的结构数据的网络界面。FoldAtlas使研究人员能够轻松地定位、查看和检索给定RNA分子的探测数据。我们还提供了在电子计算机和体内二级结构预测用于比较，在浏览器中可视化为圆图和拓扑图。目前集成到FoldAtlas中的数据来自一种新的高深度结构--拟南芥序列数据分析，与这项工作一起发布。FoldAtlas网站可访问www.foldatlas.com。根据麻省理工学院的许可，源代码可以在githorb.com/mnori/foldatlas上免费获得。原始读数数据可根据NCBI SRA加入SRP066985获得。补充数据可在生物信息学在线上获得。
Most RNA molecules form internal base pairs, leading to a folded secondary structure. Some of these structures have been demonstrated to be functionally significant. High-throughput RNA structure chemical probing methods generate millions of sequencing reads to provide structural constraints for RNA secondary structure prediction. At present, processed data from these experiments are difficult to access without computational expertise. Here we present FoldAtlas, a web interface for accessing raw and processed structural data across thousands of transcripts. FoldAtlas allows a researcher to easily locate, view, and retrieve probing data for a given RNA molecule. We also provide in silico and in vivo secondary structure predictions for comparison, visualized in the browser as circle plots and topology diagrams. Data currently integrated into FoldAtlas are from a new high-depth Structure-seq data analysis in Arabidopsis thaliana, released with this work. The FoldAtlas website can be accessed at www.foldatlas.com. Source code is freely available at github.com/mnori/foldatlas under the MIT license. Raw reads data are available under the NCBI SRA accession SRP066985. Supplementary data are available at Bioinformatics online.