Strongyloides RNA-seq Browser: a web-based software platform for on-demand bioinformatics analyses of Strongyloides species.
Strongyloides RNA-seq Browser: a web-based software platform for on-demand bioinformatics analyses of Strongyloides species.
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DOI：
10.1093/g3journal/jkab104
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发表时间：
2021-05-07
期刊：
影响因子：
--
通讯作者：
Hallem EA
中科院分区：
文献类型：
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作者：
Bryant AS;DeMarco SF;Hallem EA
土壤传播的胃肠道寄生线虫感染全球约10亿人，主要是在低资源社区。皮肤穿透胃肠道线虫属圆线虫正在成为模式系统的土壤传播蠕虫的机制研究，由于这些物种的功能基因组学工具的日益可用性。为了促进未来的类圆线虫属物种的基因组学研究，我们设计了一个基于Web的应用程序，类圆线虫RNA-seq浏览器，它提供了一个开源的，用户友好的门户网站，用于访问和分析类圆线虫基因组表达数据。具体而言，类圆线虫RNA-seq Browser利用免标记的读段映射工具和基于R的转录组学工具重新分析来自四种类圆线虫物种的公开可用的RNA测序数据集：Strongyloides stercoralis，Strongyloides ratti，Strongyloides papillosus和Strongyloides venezuelensis。该应用程序允许按需探索和量化基因表达的整个生命阶段，而不需要以前的编码经验。在这里，我们描述了这种交互式的应用程序，并演示了如何使用它可以由线虫研究人员进行一套标准的生物信息学查询。
Soil-transmitted gastrointestinal parasitic nematodes infect approximately 1 billion people worldwide, predominantly in low-resource communities. Skin-penetrating gastrointestinal nematodes in the genus Strongyloides are emerging as model systems for mechanistic studies of soil-transmitted helminths due to the growing availability of functional genomics tools for these species. To facilitate future genomics studies of Strongyloides species, we have designed a web-based application, the Strongyloides RNA-seq Browser, that provides an open source, user-friendly portal for accessing and analyzing Strongyloides genomic expression data. Specifically, the Strongyloides RNA-seq Browser takes advantage of alignment-free read mapping tools and R-based transcriptomics tools to re-analyze publicly available RNA sequencing datasets from four Strongyloides species: Strongyloides stercoralis, Strongyloides ratti, Strongyloides papillosus, and Strongyloides venezuelensis. This application permits on-demand exploration and quantification of gene expression across life stages without requiring previous coding experience. Here, we describe this interactive application and demonstrate how it may be used by nematode researchers to conduct a standard set of bioinformatics queries.