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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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Proteomics01:33

Proteomics

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
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Ribosomes01:27

Ribosomes

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Ribosomes translate genetic information encoded by messenger RNA (mRNA) into proteins. Both prokaryotic and eukaryotic cells have ribosomes. Cells that synthesize large quantities of protein—such as secretory cells in the human pancreas—can contain millions of ribosomes.
Ribosome Structure and Assembly
Ribosomes are composed of ribosomal RNA (rRNA) and proteins. In eukaryotes, rRNA is transcribed from genes in the nucleolus—a part of the nucleus that specializes in ribosome...
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Ribosomal RNA Synthesis02:53

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Ribozymes02:47

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The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
Ribozymes can...
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Protein Folding Quality Check in the RER01:29

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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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Related Experiment Video

Updated: Jul 25, 2025

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

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RiboGalaxy: A Galaxy-based Web Platform for Ribosome Profiling Data Processing - 2023 Update.

Alla D Fedorova1, Jack A S Tierney1, Audrey M Michel2

  • 1School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland; SFI Centre for Research Training in Genomics Data Science, University College Cork, Cork, Ireland.

Journal of Molecular Biology
|June 25, 2023
PubMed
Summary
This summary is machine-generated.

RiboGalaxy, a platform for ribosome profiling (Ribo-Seq) data analysis, has been updated with new tools and backend improvements. These enhancements improve data interoperability, reproducibility, and performance for Ribo-Seq studies.

Keywords:
galaxymRNA translationribo-Seqribosome profilingtranslatome

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Ribosome profiling (Ribo-Seq) provides sub-codon resolution snapshots of cellular translation.
  • It offers insights into gene expression and aids in discovering novel translated regions.
  • RiboSeq.Org is an integrated online resource for Ribo-Seq data processing and analysis.

Purpose of the Study:

  • To update the RiboGalaxy platform with new tools and backend management strategies.
  • To enhance interoperability between RiboSeq.Org resources.
  • To improve the stability, reproducibility, and performance of Ribo-Seq data analysis.

Main Methods:

  • Integration of RiboGalaxy with Trips-Viz and GWIPS-viz browsers for downstream analysis.
  • Implementation of Ansible for backend configuration management.
  • Execution of jobs within Singularity containers managed by Slurm.

Main Results:

  • Improved interoperability between RiboSeq.Org resources.
  • Enhanced stability and reproducibility of the RiboGalaxy platform.
  • Strengthened performance for Ribo-Seq data processing and analysis.

Conclusions:

  • The RiboGalaxy update significantly enhances its capabilities for Ribo-Seq data analysis.
  • The platform now offers improved integration, stability, reproducibility, and performance.
  • These advancements facilitate deeper insights into gene expression and translation.