Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

RNA secondary structure analysis using RNAstructure.

David H Mathews1

  • 1University of Rochester Medical Center, Rochester, New York, USA.

Current Protocols in Bioinformatics
|April 23, 2008
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Computational Resources for Molecular Biology 2026.

Journal of molecular biology·2026
Same author

Reparameterization of the Amber RNA Force Field Non-Bonded Terms.

bioRxiv : the preprint server for biology·2026
Same author

Nearest Neighbor Parameters for Estimating the Folding Stability of RNA Including Pseudouridine.

bioRxiv : the preprint server for biology·2026
Same author

RNA Folding Nearest Neighbor Parameters Including the Modification 1-Methyl-Pseudouridine.

bioRxiv : the preprint server for biology·2026
Same author

Motif server: web server for undesignable RNA motifs and structures.

Journal of molecular biology·2026
Same author

SamplingDesign: RNA design via continuous optimization with coupled variables and Monte-Carlo sampling.

Nature communications·2026
Same journal

Protein Sequence Analysis Using the MPI Bioinformatics Toolkit.

Current protocols in bioinformatics·2020
Same journal

Exploring Manually Curated Annotations of Intrinsically Disordered Proteins with DisProt.

Current protocols in bioinformatics·2020
Same journal

Network Building with the Cytoscape BioGateway App Explained in Five Use Cases.

Current protocols in bioinformatics·2020
Same journal

Expanding the Perseus Software for Omics Data Analysis With Custom Plugins.

Current protocols in bioinformatics·2020
Same journal

Exploring Non-Coding RNAs in RNAcentral.

Current protocols in bioinformatics·2020
Same journal

How to Illuminate the Dark Proteome Using the Multi-omic OpenProt Resource.

Current protocols in bioinformatics·2020
See all related articles

RNAstructure software predicts RNA secondary structures and identifies oligonucleotide binding sites. This user-friendly program aids in analyzing RNA interactions for research applications.

Area of Science:

  • Computational Biology
  • Molecular Biology
  • Bioinformatics

Background:

  • The secondary structure of Ribonucleic Acid (RNA) is crucial for its function.
  • Predicting RNA secondary structure and binding sites is essential for understanding RNA-mediated biological processes.
  • Existing computational tools may lack user-friendliness or comprehensive analysis capabilities.

Purpose of the Study:

  • To introduce RNAstructure, a software program for RNA secondary structure prediction and analysis.
  • To provide protocols for predicting RNA secondary structures.
  • To outline methods for predicting high-affinity oligonucleotide binding sites on structured RNA targets.

Main Methods:

  • Utilizing the RNAstructure software for computational prediction of RNA secondary structures.

Related Experiment Videos

  • Implementing algorithms for identifying potential binding sites of oligonucleotides to RNA.
  • Employing a user-friendly interface for ease of access and analysis.

    • Main Results:

    • Successful prediction of RNA secondary structures using RNAstructure.
    • Identification of high-affinity oligonucleotide binding sites on specific RNA targets.
    • Demonstration of the software's utility through provided protocols.

    Conclusions:

    • RNAstructure offers a robust and accessible platform for RNA secondary structure prediction.
    • The software facilitates the analysis of RNA-oligonucleotide interactions.
    • RNAstructure serves as a valuable tool for researchers in molecular biology and bioinformatics.