RiboSeq.Org: an integrated suite of resources for ribosome profiling data analysis and visualization

Abstract

Ribosome profiling (Ribo-Seq) has revolutionised our understanding of translation, but the increasing complexity and volume of Ribo-Seq data present challenges for its reuse. Here, we formally introduce RiboSeq.Org, an integrated suite of resources designed to facilitate Ribo-Seq data analysis and visualisation within a web browser. RiboSeq.Org comprises several interconnected tools: GWIPS-viz for genome-wide visualisation, Trips-Viz for transcriptome-centric analysis, RiboGalaxy for data processing and the newly developed RiboSeq data portal (RDP) for centralised dataset identification and access. The RDP currently hosts preprocessed datasets corresponding to 14840 sequence libraries (samples) from 969 studies across 96 species, in various file formats along with standardised metadata. RiboSeq.Org addresses key challenges in Ribo-Seq data reuse through standardised sample preprocessing, semi-automated metadata curation and programmatic information access via a REST API and command-line utilities. RiboSeq.Org enhances the accessibility and utility of public Ribo-Seq data, enabling researchers to gain new insights into translational regulation and protein synthesis across diverse organisms and conditions. By providing these integrated, user-friendly resources, RiboSeq.Org aims to lower the barrier to reproducible research in the field of translatomics and promote more efficient utilisation of the wealth of available Ribo-Seq data.

Graphical Abstract

Figure 1.. Growth of ribosome profiling data and literature.

Top: Cumulative area plot illustrating the increasing number of publicly available ribosome profiling datasets across different organisms over time. Each curve represents a distinct organism, with the area under the curve filled to facilitate visual comparison. Bottom: Bar chart displaying the yearly trend in the number of publications related to ribosome profiling or Ribo-Seq, as indicated by the presence of these terms in the title or abstract of PubMed entries. The y-axis represents the count of relevant publications for each corresponding year on the x-axis. The decrease in the number of publications after 2021 likely reflects the drop in ribosome profiling being mentioned in the abstracts rather than a decrease in its use.

Figure 2.

Metadata Landscape of RDP, A–D. Horizontal bar charts displaying the distribution of Organisms (A), inhibitors (B), tissues (C) and cell lines (D) present in the RDP Database. Each bar segment corresponds to a distinct category within the respective metadata field, with the segment width indicating the relative proportion of datasets associated with that category.