wapRNA: a web-based application for the processing of RNA sequences
wapRNA: a web-based application for the processing of RNA sequences
复制标题
wapRNA：用于处理 RNA 序列的基于网络的应用程序
DOI：
10.1093/bioinformatics/btr504
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发表时间：
2011-11-01
期刊：
影响因子：
5.8
通讯作者：
Hu, Songnian
中科院分区：
文献类型：
--
作者：
Zhao, Wenming;Liu, Wanfei;Hu, Songnian
mRNA/miRNA-seq技术正在成为全球基因表达和阐明活细胞转录调控机制的领先技术。虽然有许多工具可用于分析RNA-seq数据，但很少有工具可作为易于访问的在线web工具，用于处理基于RNA-seq的用户社区的mRNA和miRNA数据。因此，我们开发了一个综合的web应用工具来处理mRNA-seq和miRNA-seq数据。我们的网络工具wapRNA包括四个不同的模块：从SOLiD或Solexa平台测序的mRNA-seq和miRNA-seq，所有模块都在先前发表的实验数据上进行了测试。我们接受带有可选reads过滤器的原始序列数据，然后进行定位和基因注释或miRNA预测。wapRNA还集成了下游功能分析，如基因本体、KEGG通路、miRNA靶点预测和不同样品中基因或miRNA不同表达的比较。此外，我们还提供了可执行包，供用户在本地服务器上安装。
mRNA/miRNA-seq technology is becoming the leading technology to globally profile gene expression and elucidate the transcriptional regulation mechanisms in living cells. Although there are many tools available for analyzing RNA-seq data, few of them are available as easy accessible online web tools for processing both mRNA and miRNA data for the RNA-seq based user community. As such, we have developed a comprehensive web application tool for processing mRNA-seq and miRNA-seq data. Our web tool wapRNA includes four different modules: mRNA-seq and miRNA-seq sequenced from SOLiD or Solexa platform and all the modules were tested on previously published experimental data. We accept raw sequence data with an optional reads filter, followed by mapping and gene annotation or miRNA prediction. wapRNA also integrates downstream functional analyses such as Gene Ontology, KEGG pathway, miRNA targets prediction and comparison of gene's or miRNA's different expression in different samples. Moreover, we provide the executable packages for installation on user's local server.