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Updated: Nov 3, 2025
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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
Published on: February 18, 2022
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A tool for analyzing and visualizing ribo-seq data at the isoform level
Wei-Sheng Wu1, Yi-Hong Tsao2, Sheng-Cian Shiue3
1Department of Electrical Engineering, National Cheng Kung University, Tainan, 701, Taiwan. wessonwu@mail.ncku.edu.tw.
BMC Bioinformatics
|June 1, 2021
Summary
Researchers can now analyze ribosome profiling data at the isoform level using RPiso, a new software tool. This tool offers more accurate isoform abundance estimation and interactive visualization, aiding in understanding translational regulation and disease.
Area of Science:
- Molecular Biology
- Genomics
- Bioinformatics
Background:
- Translational regulation is crucial for gene expression, with its dysregulation linked to various diseases.
- Ribosome profiling (RP) is a key technique for studying translation by sequencing ribosome-protected mRNA fragments.
- Existing RP tools primarily analyze data at the gene level, limiting isoform-specific insights.
Purpose of the Study:
- To develop an accessible software tool, RPiso, for isoform-level ribosome profiling analysis.
- To provide researchers with a method for more detailed investigation of translational regulation.
Main Methods:
- Implementation of a previously developed pipeline for analyzing ribosome profiling data at the isoform level.
- Development of RPiso as an easy-to-install and execute software tool.
- Integration of a web-based viewer for interactive data visualization.
Main Results:
- RPiso offers more accurate estimation of isoform abundance compared to existing tools like Ribomap.
- The software supports analyses across a wider range of species.
- RPiso provides an interactive web-based viewer for visualizing ribosome profiling data on specific mRNA isoforms.
Conclusions:
- RPiso is a user-friendly software tool for isoform-level ribosome profiling analysis.
- The tool facilitates the analysis and visualization of ribosome profiling data, enhancing research in translational regulation.
- RPiso is expected to be a valuable resource for researchers studying gene expression and disease.
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