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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
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ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
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Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
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When we take repeated measurements on the same or replicated samples, we will observe inconsistencies in the magnitude. These inconsistencies are called errors. To categorize and characterize these results and their errors, the researcher can use statistical analysis to determine the quality of the measurements and/or suitability of the methods.
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Related Experiment Video

Updated: Jan 3, 2026

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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RiboVIEW: a computational framework for visualization, quality control and statistical analysis of ribosome profiling

Carine Legrand1,2, Francesca Tuorto1

  • 1Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany.

Nucleic Acids Research
|November 29, 2019
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Summary

Newly developed ribosome profiling methods offer detailed insights into translation. This study introduces RiboQC and RiboMine, an R pipeline for robust data quality control and analysis, overcoming computational bottlenecks.

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • High-throughput sequencing of ribosome-protected mRNA footprints enables genome-wide translational studies.
  • Computational analysis of ribosome profiling data presents a significant bottleneck for many research labs.
  • Lack of standardized pipelines for quality control and statistical analysis hinders accuracy and confidence in ribosome profiling data.

Purpose of the Study:

  • To develop automated bioinformatic and statistical tools for ribosome profiling data analysis.
  • To provide robust quality control (RiboQC) and unbiased estimation of ribosome speed (RiboMine).
  • To create an R pipeline offering an HTML interface for comprehensive data scanning.

Main Methods:

  • Development of automated bioinformatic and statistical diagnostic tools.
  • Implementation of an R pipeline integrating RiboQC and RiboMine functionalities.
  • Analysis of ribosome footprint periodicity, ligation, digestion, reproducibility, batch effects, and drug-related artifacts.

Main Results:

  • Introduction of RiboQC for robust quality control of ribosome profiling data.
  • Introduction of RiboMine for efficient and unbiased visualization of ribosome positions and speed estimation.
  • An R pipeline providing an HTML report for comprehensive data assessment, including codon enrichment and site analysis.

Conclusions:

  • The developed R pipeline addresses the computational bottleneck in ribosome profiling analysis.
  • RiboQC and RiboMine enhance the accuracy and confidence of translational studies.
  • This pipeline facilitates the optimal utilization of data from ribosome profiling experiments.