RiboPlotR

Integrated visualization of RNA-seq and Ribo-seq data in genomic context

RiboPlotR visualizes RNA-seq coverage and Ribo-seq reads across genomic coordinates for all annotated transcript isoforms of a gene. It displays transcriptional and translational signals within gene structures to facilitate comparative analysis of gene expression.

Key Features:

• RNA-seq and Ribo-seq Integration: Plots RNA-seq coverage and Ribo-seq reads together across annotated transcript isoforms.
• 3-Nucleotide Periodicity Display: Highlights 3-nt periodicity of Ribo-seq reads to reflect codon-resolved translation.
• Gene Structure Annotation: Contextualizes reads within 5′ untranslated regions (UTRs), 3′ untranslated regions (UTRs), coding sequences, and introns.
• Reading Frame Color-Coding: Differentiates reads by translation frame using three distinct colors to identify frameshifts and alternative translation events.

Scientific Applications:

• Novel Translation Event Detection: Supports identification of upstream open reading frames (uORFs) and small open reading frames (sORFs) within annotated or presumed non-coding transcripts.

Methodology:

RiboPlotR maps RNA-seq and Ribo-seq data to genomic coordinates across annotated transcript isoforms and renders coverage and frame-specific ribosome occupancy, emphasizing 3-nt periodicity within gene structural features.