Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data.
Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data.
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DOI：
10.1186/1471-2164-13-s8-s10
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发表时间：
2012
期刊：
影响因子：
4.4
通讯作者：
Liu Y
中科院分区：
文献类型：
--
作者：
Zhou A;Breese MR;Hao Y;Edenberg HJ;Li L;Skaar TC;Liu Y
选择性剪接通过表达功能不同的多种基因亚型来增加蛋白质组多样性。从RNA-seq实验中识别选择性剪接事件对于理解转录本的多样性和研究剪接的调节是重要的。我们开发了Alt Event Notebook，这是一种通过使用来自基因组引导构建工具（如Cufflinks和Scripture）的转录本注释来识别新剪接事件的工具。通过比对和转录重建工具的适当组合，Alt Event Tensor能够识别人类基因组中的新剪接事件。我们进一步对大鼠肝组织的一组RNA-seq数据应用了Alt Event technique，并确定了数十种新的盒式外显子事件，其剪接模式在大量酒精暴露后发生了变化。Alt Event Notebook能够从数据驱动的转录本注释中识别从头剪接事件，是研究剪接调控的有用工具。
Alternative splicing increases proteome diversity by expressing multiple gene isoforms that often differ in function. Identifying alternative splicing events from RNA-seq experiments is important for understanding the diversity of transcripts and for investigating the regulation of splicing. We developed Alt Event Finder, a tool for identifying novel splicing events by using transcript annotation derived from genome-guided construction tools, such as Cufflinks and Scripture. With a proper combination of alignment and transcript reconstruction tools, Alt Event Finder is capable of identifying novel splicing events in the human genome. We further applied Alt Event Finder on a set of RNA-seq data from rat liver tissues, and identified dozens of novel cassette exon events whose splicing patterns changed after extensive alcohol exposure. Alt Event Finder is capable of identifying de novo splicing events from data-driven transcript annotation, and is a useful tool for studying splicing regulation.