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Trips-Viz: a transcriptome browser for exploring Ribo-Seq data.

Stephen J Kiniry1, Patrick B F O'Connor1, Audrey M Michel1

  • 1School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.

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|September 22, 2018
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Summary
This summary is machine-generated.

Ribosome profiling (Ribo-Seq) provides insights into protein synthesis. Trips-Viz is a new tool for visualizing and analyzing Ribo-Seq data, aiding in the study of translatomes and gene expression.

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Ribosome profiling (Ribo-Seq) is a key technique for studying protein synthesis by analyzing mRNA fragments protected by ribosomes.
  • Mapping these fragments provides quantitative data on actively translated regions within the transcriptome.
  • Access to and analysis of publicly available Ribo-Seq data is crucial for advancing our understanding of translatomes.

Purpose of the Study:

  • To develop a centralized platform for accessing and visualizing publicly available ribosome profiling data.
  • To provide comprehensive graphical tools for exploring global translatome properties and individual transcript behavior.
  • To facilitate the analysis of Ribo-Seq datasets for quality control, differential gene expression, and identification of novel protein-coding elements.

Main Methods:

  • Development of Trips-Viz, a web-based visualization tool.
  • Integration of publicly available ribosome profiling datasets.
  • Implementation of graphical tools for data exploration and analysis, including quality assessment, differential expression analysis, and identification of upstream open reading frames (ORFs) and alternative proteoforms.

Main Results:

  • Trips-Viz offers a wide array of graphical tools for exploring translatome-wide and transcript-specific data.
  • The platform enables robust evaluation of Ribo-Seq dataset quality.
  • Users can perform differential gene expression analysis and visually identify upstream ORFs and alternative proteoforms.

Conclusions:

  • Trips-Viz enhances the accessibility and analytical capabilities for ribosome profiling data.
  • The tool supports in-depth investigation of global protein synthesis and individual transcript translation.
  • Trips-Viz serves as a valuable resource for researchers studying translatomes and gene expression regulation.