{"title":"RibORF: Identifying Genome-Wide Translated Open Reading Frames Using Ribosome Profiling","authors":"Zhe Ji","doi":"10.1002/cpmb.67","DOIUrl":null,"url":null,"abstract":"<p>Ribosome profiling identifies RNA fragments associated with translating ribosomes. The technology provides an opportunity to examine genome-wide translation events at single-nucleotide resolution and in an unbiased manner. Here I present a computational pipeline named RibORF to systematically identify translated open reading frames (ORFs), based on read distribution features representing active translation, including 3-nt periodicity and uniformness across codons. Analyses using the computational tool revealed pervasive translation in putative ‘noncoding’ regions, such as lncRNAs, pseudogenes, and 5′UTRs. The computational tool is useful for studying functional roles of non-canonical translation events in various biological processes. © 2018 by John Wiley & Sons, Inc.</p>","PeriodicalId":10734,"journal":{"name":"Current Protocols in Molecular Biology","volume":"124 1","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2018-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpmb.67","citationCount":"24","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Current Protocols in Molecular Biology","FirstCategoryId":"1085","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/cpmb.67","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"Biochemistry, Genetics and Molecular Biology","Score":null,"Total":0}
引用次数: 24
Abstract
Ribosome profiling identifies RNA fragments associated with translating ribosomes. The technology provides an opportunity to examine genome-wide translation events at single-nucleotide resolution and in an unbiased manner. Here I present a computational pipeline named RibORF to systematically identify translated open reading frames (ORFs), based on read distribution features representing active translation, including 3-nt periodicity and uniformness across codons. Analyses using the computational tool revealed pervasive translation in putative ‘noncoding’ regions, such as lncRNAs, pseudogenes, and 5′UTRs. The computational tool is useful for studying functional roles of non-canonical translation events in various biological processes. © 2018 by John Wiley & Sons, Inc.
RibORF:利用核糖体分析鉴定全基因组翻译开放阅读框
核糖体分析鉴定与翻译核糖体相关的RNA片段。该技术提供了以单核苷酸分辨率和无偏倚的方式检查全基因组翻译事件的机会。在这里,我提出了一个名为RibORF的计算管道,基于表示主动翻译的读取分布特征,包括3-nt周期性和密码子间的均匀性,系统地识别翻译的开放阅读帧(orf)。使用计算工具的分析显示,在假定的“非编码”区域(如lncrna、假基因和5 ' utr)中普遍存在翻译。该计算工具可用于研究非规范翻译事件在各种生物过程中的功能作用。©2018 by John Wiley &儿子,Inc。
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