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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

4.2K
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...
4.2K
Ribosomes01:27

Ribosomes

76.6K
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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Ribosomes01:27

Ribosomes

11.0K
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...
11.0K
Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

14.9K
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.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
14.9K
Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

4.4K
4.4K
pre-mRNA Processing02:01

pre-mRNA Processing

57.6K
In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a “cap” to the 5’ end of the growing transcript. In this process, a 5’ phosphate is replaced by modified guanosine that has a methyl group attached to it (7-Methyl...
57.6K

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Related Experiment Video

Updated: Feb 7, 2026

Global Identification of Co-Translational Interaction Networks by Selective Ribosome Profiling
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Global Identification of Co-Translational Interaction Networks by Selective Ribosome Profiling

Published on: October 7, 2021

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Shoelaces: an interactive tool for ribosome profiling processing and visualization.

Åsmund Birkeland1, Katarzyna ChyŻyńska2, Eivind Valen3,4

  • 1Department of Informatics, University of Bergen, Bergen, 5008, Norway.

BMC Genomics
|July 20, 2018
PubMed
Summary

Shoelaces automates ribosome profiling analysis, standardizing data processing and improving reproducibility. This toolkit identifies authentic translating footprints and P-site codons, offering visualization and pipeline integration for researchers.

Keywords:
BioinformaticsGenomicsPythonRibosome profilingTool

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Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling
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Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling

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

  • Molecular Biology
  • Bioinformatics

Background:

  • Ribosome profiling is crucial for studying translational regulation.
  • Current manual data processing is time-consuming and lacks standardization.

Purpose of the Study:

  • To develop Shoelaces, a toolkit for automating ribosome profiling data analysis.
  • To streamline processing, enhance accuracy, and improve reproducibility.

Main Methods:

  • Automated read selection and filtering based on periodicity and genomic location.
  • Automatic offset calculations for sub-codon resolution and P-site determination.
  • Development of both graphical and command-line interfaces.

Main Results:

  • Shoelaces accurately identifies translating footprints and P-site codons.
  • Analysis of 79 libraries revealed significant loss of quality data in manual pipelines.
  • The toolkit offers interactive visualization and data export in standard formats.

Conclusions:

  • Shoelaces automates and standardizes ribosome profiling analysis.
  • It enhances reproducibility through detailed logging of processing steps.
  • The freely available Python package aids researchers in efficient and accurate data analysis.