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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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Ribosomal RNA Synthesis02:53

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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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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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Riboswitches01:56

Riboswitches

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Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
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Synthetic Biology02:55

Synthetic Biology

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Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
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Related Experiment Video

Updated: Aug 23, 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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RP-REP Ribosomal Profiling Reports: an open-source cloud-enabled framework for reproducible ribosomal profiling data

Travis L Jensen1, William F Hooper1, Sami R Cherikh1

  • 1The Emmes Company, 401 North Washington Street, Suite 700, Rockville, MD 20850, USA.

F1000Research
|October 27, 2022
PubMed
Summary

Ribosomal Profiling Reports (RP-REP) is new software for analyzing protein synthesis data. It simplifies complex ribosomal profiling and RNA-Seq analysis, enabling biomarker discovery and gene response detection.

Keywords:
AMIRNA-SeqRP-REPcloud computingdifferential gene translationpathway enrichmentreproducible researchribosomal profilingtranscriptomicstranslational efficiency

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Area of Science:

  • Genomics
  • Computational Biology
  • Molecular Biology

Background:

  • Ribosomal profiling measures global protein synthesis, crucial for biomarker discovery.
  • Analyzing this data requires specialized preprocessing and statistical methods.
  • Existing tools lack comprehensive, user-friendly solutions for end-to-end analysis.

Purpose of the Study:

  • To introduce Ribosomal Profiling Reports (RP-REP), an open-source, cloud-enabled software.
  • To provide a streamlined pipeline for gene-level ribosomal profiling and RNA-Seq analysis.
  • To facilitate biomarker discovery and the identification of treatment-responsive genes.

Main Methods:

  • RP-REP software executed on AWS or Ubuntu Linux servers.
  • Analysis of FASTQ files from local, AWS S3, or SRA storage.
  • Automated steps: RNA filtering, footprint enrichment, alignment, quantification, QC, normalization, visualization, differential translation analysis.

Main Results:

  • RP-REP successfully processed ribosomal profiling and RNA-Seq data.
  • The software generated comprehensive PDF reports and publication-ready figures.
  • Demonstrated utility via a dengue virus infection study case.

Conclusions:

  • RP-REP offers a powerful, accessible solution for analyzing ribosomal profiling data.
  • The software simplifies complex analyses, aiding in biological insights.
  • RP-REP supports biomarker discovery and understanding gene responses to treatments.