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

Automatic display of RNA secondary structures

G Muller1, C Gaspin, A Etienne

  • 1UPR Structure des Macromolécules Biologues et Mécanismes de Reconnaissance, Institut de Biologie Moléulaire et Cellulaire du CNRS, Strasbourg, France.

Computer Applications in the Biosciences : CABIOS
|October 1, 1993
PubMed
Summary

New C programs generate clear, non-overlapping ribonucleic acid secondary structure displays. These tools, rnasearch and rnadisplay, aid in visualizing and comparing RNA folding patterns.

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

Increase in early syphilis diagnoses in the young heterosexual population of Reunion Island: surveillance data, 2010-2018.

Journal of the European Academy of Dermatology and Venereology : JEADV·2021
Same author

Mapping rRNA 2'-O-methylations and identification of C/D snoRNAs in Arabidopsis thaliana plants.

RNA biology·2021
Same author

Reverse Monte Carlo reconstruction algorithm for discrete electron tomography based on HAADF-STEM atom counting.

Journal of microscopy·2016
Same author

Predictors of early outcome after acute appendicitis: is delaying surgery for acute appendicitis an option? A retrospective study.

European journal of trauma and emergency surgery : official publication of the European Trauma Society·2016
Same author

Interstitial laser photocoagulation for the treatment of osteoid osteoma: retrospective study on 35 cases.

Diagnostic and interventional imaging·2013
Same author

What controls fleshy fruit acidity? A review of malate and citrate accumulation in fruit cells.

Journal of experimental botany·2013

Area of Science:

  • Computational biology
  • Bioinformatics
  • Molecular biology

Background:

  • Visualizing ribonucleic acid (RNA) secondary structures is crucial for understanding their function.
  • Existing methods for displaying RNA structures can be complex and may result in overlapping or unclear visualizations.
  • Efficient tools are needed to analyze and compare different predicted RNA folding patterns.

Purpose of the Study:

  • To develop a suite of C programs for generating compact, non-overlapping, and visually appealing displays of RNA secondary structures.
  • To provide tools for dynamic rearrangement of overlapping structural elements and facilitate comparison of predicted RNA folds.
  • To enable graphical and hardcopy output of RNA secondary structures, with options for data annotation.

Main Methods:

Related Experiment Videos

  • Development of the 'rnasearch' program implementing a novel dynamic rearrangement algorithm for resolving overlapping structures.
  • Utilization of the GL library and UNIX environment for program development.
  • Creation of 'rnadisplay' for graphical workstation visualization and 'print2D' for PostScript file generation.
  • Incorporation of labeling capabilities for integrating chemical modification and enzymatic cleavage data.

    • Main Results:

    • Successful generation of compact and non-overlapping displays for various RNA secondary structures.
    • Demonstrated efficiency of the 'rnasearch' algorithm, with a 16S rRNA (1542 bases) analysis completed in 38.6 seconds.
    • Validated the utility of the programs through applications to RNaseP, 5S rRNA, and 16S rRNA structures.
    • Enabled clear visualization and comparison of different predicted RNA folding patterns.

    Conclusions:

    • The developed C programs offer an efficient and effective solution for visualizing RNA secondary structures.
    • These tools enhance the ability to analyze, compare, and interpret RNA folding, aiding in functional studies.
    • The software provides a valuable resource for researchers in molecular biology and bioinformatics working with RNA structures.