By capturing and sequencing the RNA fragments protected by translating ribosomes, ribosome profiling provides snapshots of translation at subcodon resolution. The growing needs for comprehensive annotation and characterization of the context-dependent translatomes are calling for an efficient and unbiased method to accurately recover the signal of active translation from the ribosome profiling data. Here we present our new method, RiboCode, for such purpose. Being tested with simulated and real ribosome profiling data, and validated with cell type-specific QTI-seq and mass spectrometry data, RiboCode exhibits superior efficiency, sensitivity, and accuracy for de novo annotation of the translatome, which covers various types of ORFs in the previously annotated coding and non-coding regions. As an example, RiboCode was applied to assemble the context-specific translatomes of yeast under normal and stress conditions. Comparisons among these translatomes revealed stress-activated novel upstream and downstream ORFs, some of which are associated with translational dysregulations of the annotated main ORFs under the stress conditions.

中文翻译：

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从头开始注释和鉴定带有核糖体图谱数据的翻译组

通过捕获和测序受翻译核糖体保护的RNA片段，核糖体谱提供了亚密码子分辨率的翻译快照。对上下文相关翻译组的全面注释和表征的需求不断增长，这要求一种有效且无偏见的方法来从核糖体图谱数据中准确恢复主动翻译的信号。为此，我们展示了我们的新方法RiboCode。用模拟和实际核糖体分析数据被测试，并与细胞类型特异性QTI-SEQ和质谱数据证实，RiboCode表现出优异的效率，灵敏度和准确度从头译本的注释，涵盖了先前注释的编码和非编码区域中的各种类型的ORF。例如，在正常和压力条件下，使用RiboCode组装酵母的上下文特定翻译组。这些翻译组之间的比较揭示了应力激活的新型上游和下游ORF，其中一些与在压力条件下带注释的主要ORF的翻译失调有关。