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从头使用核糖体分析数据识别主动翻译的开放阅读框

JoVE Journal
Biology
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JoVE Journal Biology

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

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从头使用核糖体分析数据识别主动翻译的开放阅读框

DOI:

10.3791/63366-v

•

08:23 min

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February 18, 2022

•

Yanan Zhu*¹, Fajin Li*^2,3, Xuerui Yang³, Zhengtao Xiao

¹School of Basic Medical Sciences,Xi’an Jiaotong University Health Science Center, ²MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences,Tsinghua University, ³Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science

Chapters

00:04Introduction
01:01Environment Setup and RiboCode Installation
01:23Data Preparation
03:35Removing Ribosomal RNA Contamination
03:59Aligning the Clean Reads to the Genome
04:25Size Selection of Ribosome Protected Fragments, Identification of P-Sites, and De novo Annotate Translating Open Reading Frames
04:59Results: Identification of the Novel Open Reding Frames (ORFs) with the Application of RiboCode
07:20Conclusion

Summary

Automatic Translation

翻译核糖体将每个密码子的三个核苷酸解码为肽。它们沿着mRNA的运动，通过核糖体分析捕获，产生表现出特征性三重态周期性的足迹。该协议描述了如何使用RiboCode从核糖体分析数据中破译这一突出特征，以识别全转录组水平上主动翻译的开放阅读框。

Tags

Keywords: Ribosome Profiling Translation Open Reading Frames Genome-wide RiboCode MRNA Annotation RRNA Sequence Read Archive Alignment

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