JNSViewer-A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures.
JNSViewer-A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures.
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DOI：
10.1371/journal.pone.0179040
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发表时间：
2017
期刊：
影响因子：
3.7
通讯作者：
Liang C
中科院分区：
文献类型：
--
作者：
Shi J;Li X;Dong M;Graham M;Yadav N;Liang C
许多工具可用于可视化RNA或DNA二级结构，但在JavaScript中很少实现与日益流行的Web计算平台的无缝集成。我们已经开发了JNSViewer，一个高度交互式的Web服务，这是捆绑了几个流行的DNA/RNA二级结构预测工具，可以提供精确的和交互式的核苷酸，点括号数据，二级结构图和基因注释之间的对应关系。在JNSViewer中，用户可以使用不同的程序和设置进行RNA二级结构预测，以GFF格式将定制的基因注释添加到结构图中，搜索特定的线性基序，并提取子序列的相关结构图。JNSViewer还允许用户选择拟南芥基因组序列的转录本或特定片段，并预测相应的二级结构。流行的基因组浏览器（即，JBrowse和BrowserGenome）集成到JNSViewer中，以提供染色体位置、基因注释和二级结构的强大可视化。此外，我们使用默认设置的StructureFold通过结合体内高通量RNA结构分析数据来预测拟南芥的一些RNA结构，并将结果存储在我们的Web服务器中，这可能是植物RNA二级结构研究的有用资源。JNSViewer可从http://bioinfolab.miamioh.edu/jnsviewer/index.html获得。
Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and interactive correspondence among nucleotides, dot-bracket data, secondary structure graphs, and genic annotations. In JNSViewer, users can perform RNA secondary structure predictions with different programs and settings, add customized genic annotations in GFF format to structure graphs, search for specific linear motifs, and extract relevant structure graphs of sub-sequences. JNSViewer also allows users to choose a transcript or specific segment of Arabidopsis thaliana genome sequences and predict the corresponding secondary structure. Popular genome browsers (i.e., JBrowse and BrowserGenome) were integrated into JNSViewer to provide powerful visualizations of chromosomal locations, genic annotations, and secondary structures. In addition, we used StructureFold with default settings to predict some RNA structures for Arabidopsis by incorporating in vivo high-throughput RNA structure profiling data and stored the results in our web server, which might be a useful resource for RNA secondary structure studies in plants. JNSViewer is available at http://bioinfolab.miamioh.edu/jnsviewer/index.html.