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

Structural analysis of aligned RNAs.

Björn Voss1

  • 1Experimental Bioinformatics, Institute of Biology II, Freiburg University, Schänzlestrasse 1, 79104 Freiburg, Germany. bjoern.voss@biologie.uni-freiburg.de

Nucleic Acids Research
|October 6, 2006
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

Thorough RNA Interactome Data Analysis Based on Direct Duplex Detection Data.

Methods in molecular biology (Clifton, N.J.)·2025
Same author

Metagenomic CRISPR Array Analysis Tool: a novel graph-based approach to finding CRISPR arrays in metagenomic datasets.

microLife·2025
Same author

Transcriptional regulators ensuring specific gene expression and decision-making at high TGFβ doses.

Life science alliance·2024
Same author

Classified Dynamic Programming in RNA Structure Analysis.

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

RNA interaction format: a general data format for RNA interactions.

Bioinformatics (Oxford, England)·2023
Same author

A Small RNA Is Linking CRISPR-Cas and Zinc Transport.

Frontiers in molecular biosciences·2021
Same journal

Correction to 'scSuperAnnotator: A platform for benchmarking comparison and visualizing automated cellular annotation methods for scRNA-seq data'.

Nucleic acids research·2026
Same journal

Correction to 'Differentiable partition function calculation for RNA'.

Nucleic acids research·2026
Same journal

Deployment of non-canonical splicing in tunicate genomes is mediated by divergent U2AF function and changing m6A modification in U1 and U6 snRNA.

Nucleic acids research·2026
Same journal

Bacillus subtilis DnaB forms multiple protein-protein interactions essential for DNA replication initiation.

Nucleic acids research·2026
Same journal

Multiple forms of protein-protein and DNA binding are exhibited by BrxC from the BREX phage restriction system.

Nucleic acids research·2026
Same journal

Biosynthesis of glycosylated 5-hydroxycytosine in the DNA of diverse viruses.

Nucleic acids research·2026
See all related articles

RNAlishapes analyzes non-coding RNA (ncRNA) structures, identifying distinct conformations. This tool aids in understanding RNA classes and predicting consensus structures from sequence alignments.

Area of Science:

  • * Molecular Biology
  • * Bioinformatics
  • * Structural Biology

Background:

  • * Non-coding RNAs (ncRNAs) are crucial molecules with structure defining their function.
  • * Detailed structural analysis is essential for characterizing ncRNA classes.
  • * Existing methods require enhancement for comparative structural analysis.

Purpose of the Study:

  • * To introduce RNAlishapes, a novel tool for detailed structural analysis of ncRNA classes.
  • * To integrate secondary structure prediction with comparative sequence analysis.
  • * To provide a robust method for consensus structure prediction.

Main Methods:

  • * RNAlishapes combines suboptimal folding and shape abstraction with RNA alignment folding.
  • * Utilizes an extended thermodynamic model and covariance scoring for paired base analysis.

Related Experiment Videos

  • * Employs shape abstraction for analyzing bacterial trp-operon leader sequences.

    • Main Results:

    • * RNAlishapes successfully identified two alternating conformations in bacterial trp-operon leaders.
    • * The tool demonstrates good prediction accuracy for RNA structures.
    • * Provides in-depth analysis capabilities for aligned RNA sequences.

    Conclusions:

    • * RNAlishapes offers a powerful platform for the structural analysis of ncRNA classes.
    • * It serves as a reliable method for predicting consensus RNA structures from alignments.
    • * The tool is accessible for online use and download, facilitating broader research applications.