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Related Concept Videos

Ribosome Profiling02:24

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RiboParser/RiboShiny: an integrated platform for comprehensive analysis and visualization of Ribo-seq data.

Shuchao Ren1, Yinan Li1, Zhipeng Zhou1

  • 1National Key Laboratory of Agricultural Microbiology, College of Life Science, Huazhong Agricultural University, Wuhan, Hubei 430070, China.

Journal of Genetics and Genomics = Yi Chuan Xue Bao
|April 23, 2025
PubMed
Summary

We developed RiboParser/RiboShiny, a user-friendly framework to analyze and visualize ribosome profiling (Ribo-seq) data. This tool enhances the accuracy and efficiency of interpreting translational regulation, advancing gene expression studies.

Keywords:
Data visualizationDifferentially translated genesP-site detectionRibo-seqRibosome profilingSelective Ribo-seqTranslationTranslation elongation speed

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Ribosome profiling (Ribo-seq) has revolutionized the study of in vivo translational regulation.
  • Analyzing and visualizing Ribo-seq data presents significant challenges, necessitating improved computational tools.
  • Existing analytical pipelines often lack comprehensiveness, accuracy, and user-friendliness.

Purpose of the Study:

  • To develop a robust and user-friendly framework, RiboParser/RiboShiny, for the comprehensive analysis and visualization of Ribo-seq data.
  • To enhance the accuracy and stability of P-site detection in Ribo-seq analysis, particularly for challenging transcript types.
  • To provide a universally applicable platform for diverse organisms with sequenced genomes.

Main Methods:

  • Optimization of ribosome structure-based and start/stop-based models for P-site detection.
  • Development of RiboParser for comprehensive Ribo-seq data analyses (QC, gene-level, codon-level, variants).
  • Creation of RiboShiny for adaptable and user-friendly Ribo-seq data visualization.

Main Results:

  • RiboParser/RiboShiny framework significantly improves P-site detection accuracy and stability.
  • The platform offers comprehensive analytical modules, including quality control and various levels of gene analysis.
  • RiboShiny provides intuitive visualization tools for exploring the translational landscape.

Conclusions:

  • RiboParser/RiboShiny offers a powerful, integrated solution for Ribo-seq data analysis and visualization.
  • The framework enhances the precision and efficiency of interpreting translational regulation.
  • This tool has the potential to significantly advance research in gene expression and molecular biology.