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Related Concept Videos

Riboswitches01:56

Riboswitches

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...
Ribosome Profiling02:24

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RNA-seq03:21

RNA-seq

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Ribozymes02:47

Ribozymes

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 be...
Ribozymes02:47

Ribozymes

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 be...
Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

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Related Experiment Video

Updated: Jun 11, 2026

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
10:52

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

Published on: September 28, 2017

RKB: a Semantic Web knowledge base for RNA.

Jose Cruz-Toledo1, Michel Dumontier, Marc Parisien

  • 1Department of Biology, Carleton University 1125 Colonel By Drive, K1S5B6, Ottawa, Canada . jctoledo@connect.carleton.ca.

Journal of Biomedical Semantics
|July 15, 2010
PubMed
Summary
This summary is machine-generated.

A new RNA knowledge base (RKB) integrates diverse RNA data using Semantic Web technologies. This structure enables expert question answering over RNA structure and function information.

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Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing (RIPiT-Seq)
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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

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Related Experiment Videos

Last Updated: Jun 11, 2026

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
10:52

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

Published on: September 28, 2017

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing (RIPiT-Seq)
09:26

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing (RIPiT-Seq)

Published on: July 10, 2019

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Advanced understanding of RNA structure and function necessitates integrated knowledge representation.
  • Existing formats like RNAML lack domain-specific semantics for expert querying.
  • Independent data sources (genome sequencing, microarray, SELEX) require a unified approach.

Purpose of the Study:

  • To develop an inclusive knowledge representation for RNA structure-based knowledge.
  • To leverage RDF/OWL Semantic Web technologies for RNA data integration.
  • To enable expert question answering over diverse RNA information.

Main Methods:

  • Developed an RNA knowledge base (RKB) using RDF/OWL Semantic Web technologies.
  • Extended existing ontologies with RNA-specific terminology and structural features.
  • Populated RKB with data from PDB entries and MC-Annotate structural annotations.
  • Utilized description logic reasoning for querying the knowledge base.

Main Results:

  • Created a comprehensive RNA knowledge base (RKB) for structure-based information.
  • RKB incorporates terminology for nucleic acid composition and structural features.
  • Demonstrated the capability of RKB to answer complex queries using reasoning.

Conclusions:

  • Semantic Web technologies provide a robust framework for integrating RNA knowledge.
  • RKB facilitates question answering over independently published RNA data.
  • This approach enhances the integration and accessibility of RNA structural information.