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 Concept Videos

Introduction to R01:11

Introduction to R

R is a powerful software environment for statistical computing and graphics. Originating as an implementation of the S language, developed at Bell Laboratories, R has evolved into a robust, open-source statistical software favored by statisticians and data scientists worldwide. Its comprehensive suite includes data manipulation, calculation, and graphical display capabilities, making it versatile for data analysis and visualization. Its programming language is at the core of R's functionality,...
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
RNA Structure01:19

RNA Structure

The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

You might also read

Related Articles

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

Sort by
Same author

Splicing dependency between EIF4G2 introns is mediated by exon definition and relies on a downstream splicing event.

The Journal of biological chemistry·2026
Same author

DuplexDiscoverer: a computational method for the analysis of experimental duplex RNA-RNA interaction data.

Nucleic acids research·2025
Same author

Chlorhexidine for ocular antisepsis before intravitreal injection: A systematic review and meta-analysis.

Survey of ophthalmology·2025
Same author

Luminal breast epithelial cells of BRCA1 or BRCA2 mutation carriers and noncarriers harbor common breast cancer copy number alterations.

Nature genetics·2024
Same author

Integrated single cell analysis reveals co-evolution of malignant B cells and tumor micro-environment in transformed follicular lymphoma.

Cancer cell·2024
Same author

Single-cell decoding of drug induced transcriptomic reprogramming in triple negative breast cancers.

Genome biology·2024

Related Experiment Video

Updated: May 23, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

R-CHIE: a web server and R package for visualizing RNA secondary structures.

Daniel Lai1, Jeff R Proctor, Jing Yun A Zhu

  • 1Department of Computer Science, Centre for High-Throughput Biology, University of British Columbia, Vancouver V6T 1Z4, Canada.

Nucleic Acids Research
|March 22, 2012
PubMed
Summary
This summary is machine-generated.

Visualizing RNA secondary structures with arc diagrams offers a new method for understanding RNA function and improving prediction algorithms. This approach effectively displays complex structures, including pseudo-knots, and aids in comparing sequence and structure conservation.

More Related Videos

RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Related Experiment Videos

Last Updated: May 23, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Visual examination of RNA structures is crucial for understanding function and evaluating prediction algorithms.
  • Current methods often represent RNA secondary structures as planar stem-loop diagrams.
  • These planar representations can be limiting for complex or non-standard RNA structures.

Purpose of the Study:

  • To introduce an alternative method for visualizing RNA secondary structures using arc diagrams.
  • To provide a visualization tool capable of handling complex RNA structures, including pseudo-knots.
  • To facilitate the comparison of RNA secondary structures and integrate structural information with sequence data.

Main Methods:

  • Development of an arc diagram visualization method for RNA secondary structures.
  • Implementation of the visualization algorithm as a web server (R-chie) and an R package (R4RNA).
  • Demonstration of the ability to display pseudo-knotted, transient, and alternative structural features.

Main Results:

  • Arc diagrams provide an intuitive representation for RNA secondary structures, especially those difficult to depict with traditional methods.
  • The R-chie web server and R4RNA package enable local and remote visualization of RNA structures.
  • The method allows for direct comparison of known and predicted RNA structures alongside multiple sequence alignments.

Conclusions:

  • Arc diagrams offer a versatile and intuitive approach to visualizing RNA secondary structures.
  • The developed tools (R-chie and R4RNA) enhance the study of RNA structure-function relationships and prediction algorithm evaluation.
  • This visualization method aids in identifying conserved structural and sequence elements in RNA molecules.