RiboPlotR: a visualization tool for periodic Ribo-seq reads

Plant Methods

Hsin-Yen Larry Wu¹  Polly Yingshan Hsu¹ 

[1]Department of Biochemistry & Molecular Biology, Michigan State University, 48824, East Lansing, MI, USA

关键词: Ribo-seq;    3-nucleotide periodicity;    Isoform;    Upstream ORF;    Small ORF;   

DOI  :  10.1186/s13007-021-00824-4

来源: Springer

【 摘 要 】

BackgroundRibo-seq has revolutionized the study of genome-wide mRNA translation. High-quality Ribo-seq data display strong 3-nucleotide (nt) periodicity, which corresponds to translating ribosomes deciphering three nts at a time. While 3-nt periodicity has been widely used to study novel translation events such as upstream ORFs in 5′ untranslated regions and small ORFs in presumed non-coding RNAs, tools that allow the visualization of these events remain underdeveloped.ResultsRiboPlotR is a visualization package written in R that presents both RNA-seq coverage and Ribo-seq reads in genomic coordinates for all annotated transcript isoforms of a gene. Specifically, for individual isoform models, RiboPlotR plots Ribo-seq data in the context of gene structures, including 5′ and 3′ untranslated regions and introns, and it presents the reads for all three reading frames in three different colors. The inclusion of gene structures and color-coding the reading frames facilitate observing new translation events and identifying potential regulatory mechanisms.ConclusionsRiboPlotR is freely available (https://github.com/hsinyenwu/RiboPlotR and https://sourceforge.net/projects/riboplotr/) and allows the visualization of translated features identified in Ribo-seq data.

【 授权许可】

CC BY