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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
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Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

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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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Ribozymes02:47

Ribozymes

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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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X-ray Diffraction of Biological Samples01:10

X-ray Diffraction of Biological Samples

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X-ray diffraction or XRD is an analytical tool that utilizes X-rays to study ordered structures such as crystalline organic and inorganic samples, polycrystalline materials, proteins, carbohydrates, and drugs.
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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.
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RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing
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RiboGraph: An interactive visualization system for ribosome profiling data at read length resolution.

Jonathan Chacko1, Hakan Ozadam1,2, Can Cenik1

  • 1Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.

Biorxiv : the Preprint Server for Biology
|January 23, 2024
PubMed
Summary
This summary is machine-generated.

RiboGraph is a new tool for visualizing ribosome occupancy data, offering real-time analysis without lengthy preprocessing. It simplifies complex ribosome profiling data visualization for researchers.

Keywords:
InteractiveRiboRibo-SeqRibosome profilingSoftwareTranslationVisualization

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Area of Science:

  • Molecular Biology
  • Bioinformatics

Background:

  • Ribosome profiling measures ribosome occupancy at nucleotide resolution.
  • Analyzing this data presents visualization and analysis challenges due to its complexity.

Approach:

  • Introduced RiboGraph, a visualization tool for ribosome occupancy data.
  • RiboGraph utilizes a specialized, compact .ribo file format.
  • Eliminates the need for data preprocessing and large alignment files.

Key Points:

  • Enables interactive, real-time visualization at ribosome-protected fragment length resolution.
  • Operates on a compact file type for enhanced efficiency.
  • Provides an integrated toolset for comprehensive visual analysis.

Conclusions:

  • RiboGraph overcomes challenges in visualizing ribosome profiling data.
  • Facilitates efficient and interactive analysis of ribosome occupancy.
  • Empowers researchers with a dedicated tool for visual data exploration.