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

Nucleic Acid Structure01:25

Nucleic Acid Structure

6.3K
The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
6.3K
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

3.8K
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...
3.8K
RNA-seq03:21

RNA-seq

10.2K
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...
10.2K
Nucleic acids02:43

Nucleic acids

164.3K
Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes,...
164.3K

You might also read

Related Articles

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

Sort by
Same author

On the Number of Control Nodes in Boolean Networks With Degree Constraints.

IEEE transactions on cybernetics·2026
Same author

DiCleavePlus: A Transformer-Based Model to Detect Human Dicer Cleavage Sites Within Cleavage Patterns.

Genes to cells : devoted to molecular & cellular mechanisms·2025
Same author

A TROP2-targeting ADC synergizes with oxidative phosphorylation inhibitor to enhance apoptosis in ESCC by suppressing the PI3K-AKT-mTOR signaling pathway.

Cell death & disease·2025
Same author

Toward Environment-Sensitive Molecular Inference via Mixed Integer Linear Programming.

ACS omega·2025
Same author

Enhancing epidemic forecasting with a physics-informed spatial identity neural network.

PloS one·2025
Same author

Cycle-configuration descriptors: a novel graph-theoretic approach to enhancing molecular inference.

Journal of cheminformatics·2025

Related Experiment Video

Updated: Aug 12, 2025

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

31.6K

Metrics for RNA Secondary Structure Comparison.

Feiqi Wang1, Tatsuya Akutsu2, Tomoya Mori3

  • 1Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan.

Methods in Molecular Biology (Clifton, N.J.)
|January 27, 2023
PubMed
Summary
This summary is machine-generated.

Comparing complex RNA secondary structures with pseudoknots is now feasible. Our new algorithm and software enable accurate analysis of these vital RNA structures, advancing functional studies.

Keywords:
PseudoknotRNA secondary structureTopological centroidTree edit distance

More Related Videos

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

4.4K
An Assay for Quantifying Protein-RNA Binding in Bacteria
07:02

An Assay for Quantifying Protein-RNA Binding in Bacteria

Published on: June 12, 2019

6.7K

Related Experiment Videos

Last Updated: Aug 12, 2025

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

31.6K
Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

4.4K
An Assay for Quantifying Protein-RNA Binding in Bacteria
07:02

An Assay for Quantifying Protein-RNA Binding in Bacteria

Published on: June 12, 2019

6.7K

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Computational Biology

Background:

  • RNA secondary structures are crucial for RNA function.
  • Pseudoknotted RNA structures are biologically important but computationally challenging.
  • Current methods struggle with the complexity of pseudoknotted RNA structures.

Purpose of the Study:

  • To develop a novel algorithm and metric for comparing pseudoknotted RNA secondary structures.
  • To create user-friendly software for analyzing these complex RNA structures.
  • To overcome the limitations of existing in silico methods for RNA structure comparison.

Main Methods:

  • Topological centroid identification for structural analysis.
  • Tree edit distance metric for quantitative comparison.
  • Development of a publicly available software tool for Microsoft Windows and Apple macOS.

Main Results:

  • Successful implementation of an algorithm and metric for pseudoknotted RNA secondary structure comparison.
  • A functional software tool is now available for researchers.
  • The method effectively handles the complexity of pseudoknots.

Conclusions:

  • The developed algorithm and software provide a robust solution for comparing pseudoknotted RNA secondary structures.
  • This facilitates deeper understanding of RNA functions and their correlation with structure.
  • The tool is accessible to the scientific community for advancing RNA research.