Riborex: fast and flexible identification of differential translation from Ribo-seq data
Riborex: fast and flexible identification of differential translation from Ribo-seq data
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DOI：
10.1093/bioinformatics/btx047
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发表时间：
2017-06-01
期刊：
影响因子：
5.8
通讯作者：
Smith, Andrew D.
中科院分区：
文献类型：
--
作者：
Li, Wenzheng;Wang, Weili;Smith, Andrew D.
动机：最近核糖体图谱或Ribo-seq技术的发展使翻译调控的全球分析成为可能。这种方法提供了特定生物样本中每个表达基因的核糖体活性图谱。当结合匹配的RNA-seq基因表达谱分析Ribo-seq数据时，产生翻译效率的测量。现有的识别跨样本差异翻译基因的计算方法是基于合理的原则，但需要用户在精度和速度之间进行选择。结果：我们提出了Riborex，一个用于绘制基因组范围翻译效率差异的计算工具。Riborex与现有方法有类似的数学结构，但有一个简化的实现。Riborex直接利用已建立的RNA-SEQ分析框架进行所有参数估计，为用户提供了用于这些计算的强大引擎选择。其结果是一种在不牺牲准确性的情况下显著快于现有方法的方法。补充信息：补充数据可在生物信息学在线上获得。
Motivation: Global analysis of translation regulation has recently been enabled by the development of Ribosome Profiling, or Ribo-seq, technology. This approach provides maps of ribosome activity for each expressed gene in a given biological sample. Measurements of translation efficiency are generated when Ribo-seq data is analyzed in combination with matched RNA-seq gene expression profiles. Existing computational methods for identifying genes with differential translation across samples are based on sound principles, but require users to choose between accuracy and speed.Results: We present Riborex, a computational tool for mapping genome-wide differences in translation efficiency. Riborex shares a similar mathematical structure with existing methods, but has a simplified implementation. Riborex directly leverages established RNA-seq analysis frameworks for all parameter estimation, providing users with a choice among robust engines for these computations. The result is a method that is dramatically faster than available methods without sacrificing accuracy.Supplementary information: Supplementary data are available at Bioinformatics online.