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

Secondary structure prediction for aligned RNA sequences.

Ivo L Hofacker1, Martin Fekete, Peter F Stadler

  • 1Institut für Theoretische Chemie, Universität Wien, Währingerstrasse 17, Austria.

Journal of Molecular Biology
|June 25, 2002
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

Rational design of mechanically active RNAs: de novo engineering of functional exoribonuclease-resistant RNAs.

Nucleic acids research·2026
Same author

Sequence Design for RNA-RNA Interactions.

Methods in molecular biology (Clifton, N.J.)·2024
Same author

Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data.

Nucleic acids research·2024
Same author

tRNA expression and modification landscapes, and their dynamics during zebrafish embryo development.

Nucleic acids research·2024
Same author

Comparative RNA Genomics.

Methods in molecular biology (Clifton, N.J.)·2024
Same author

The Multiscale Ernwin/SPQR RNA Structure Prediction Pipeline.

Methods in molecular biology (Clifton, N.J.)·2024
Same journal

Clinical inflammasome biomarkers: Progress and prospects.

Journal of molecular biology·2026
Same journal

Biologically Relevant, Cationic Residues in Human Rhinovirus Stabilize Capsid-Bound RNA Duplexes, and Restrict Capsid Flexibility.

Journal of molecular biology·2026
Same journal

Cryo-EM structures of phage T4 infection intermediate.

Journal of molecular biology·2026
Same journal

A classic fold with a twist: Structural architecture of Dhillonvirus phage Bas18.

Journal of molecular biology·2026
Same journal

Tesorai Search: cloud-based database search engine boosts identifications for mass spectrometry proteomics with a pretrained peptide-spectrum deep-learning model.

Journal of molecular biology·2026
Same journal

Characterization of diverse functions of NRF1 nuclear localization sequence.

Journal of molecular biology·2026
See all related articles

This study introduces a novel method to predict RNA secondary structures using thermodynamic stability and sequence covariation. The approach achieves high prediction reliability, aiding in understanding functional RNA conservation.

Area of Science:

  • Computational Biology
  • Molecular Biology
  • Bioinformatics

Background:

  • Functional RNA molecules exhibit conserved secondary structures crucial for their biological roles.
  • Understanding these structures is key to deciphering RNA function and evolution.
  • Existing methods may not fully integrate thermodynamic principles with evolutionary sequence data.

Purpose of the Study:

  • To develop and present a computational method for determining the consensus secondary structure of aligned RNA sequences.
  • To incorporate both thermodynamic stability and sequence covariation into structure prediction.
  • To assess the accuracy and applicability of the developed method.

Main Methods:

  • A novel algorithm was developed to compute RNA consensus secondary structures.

Related Experiment Videos

  • The method integrates thermodynamic stability predictions with analysis of sequence covariation across aligned RNA sequences.
  • The approach was validated by comparing predicted structures with known phylogenetic structures of ribosomal RNAs (rRNAs).

    • Main Results:

    • The method demonstrated a prediction reliability exceeding 80% with as few as five related RNA sequences.
    • Application to Early Noduline messenger RNA (mRNA) revealed significant secondary structure.
    • This predicted secondary structure for Early Noduline mRNA was robustly supported by observed sequence covariation.

    Conclusions:

    • The presented computational method accurately predicts RNA secondary structures by combining thermodynamic and evolutionary information.
    • The findings highlight the importance of conserved secondary structures in functional RNAs, exemplified by Early Noduline mRNA.
    • This tool offers a reliable approach for RNA structure prediction, advancing research in molecular biology and bioinformatics.