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

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 has a double-helix structure. The...
Structural Classification of Joints01:20

Structural Classification of Joints

Joints, also known as articulations, are classified based on their structural characteristics, i.e., based on whether the articulating surfaces of the adjacent bones are directly connected by fibrous connective tissue or cartilage, or whether the articulating surfaces contact each other within a fluid-filled joint cavity. These differences serve to divide the joints of the body into three structural classifications.
A fibrous joint is where the adjacent bones are united by fibrous connective...
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...
Structural Isomerism02:34

Structural Isomerism

Isomerism in Complexes
Isomers are different chemical species that have the same chemical formula. Structural isomerism of coordination compounds can be divided into two subcategories, the linkage isomers and coordination-sphere isomers.
Linkage isomers occur when the coordination compound contains a ligand that can bind to the transition metal center through two different atoms. For example, the CN− ligand can bind through the carbon atom or through the nitrogen atom. Similarly, SCN− can be...

You might also read

Related Articles

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

Sort by
Same author

Detecting bias in algorithms used to disseminate information in social networks and mitigating it using multiobjective optimization.

PNAS nexus·2025
Same author

Complex In Silico RNA Design with MoiRNAiFold.

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

ePyDGGA: automatic configuration for fitting epidemic curves.

Scientific reports·2024
Same author

Macrophage inflammation resolution requires CPEB4-directed offsetting of mRNA degradation.

eLife·2022
Same author

Correction to 'MoiRNAiFold: a novel tool for complex in silico RNA design'.

Nucleic acids research·2021
Same author

Resiliency of on-demand multimodal transit systems during a pandemic.

Transportation research. Part C, Emerging technologies·2021
Same journal

Trust, Reproducibility, and Progress: The Roles of Independent Blind Prediction and Assessment and Benchmarking in Computational Biology.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
Same journal

The Evolving Cyberinfrastructure at the National Institutes of Health to Support Data and AI in Biomedical Research.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
Same journal

Applications of AI & ML in Biomanufacturing of Cell and Gene Therapies.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
Same journal

AI for Health: Leveraging Artificial Intelligence to Revolutionize Healthcare.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
Same journal

Workshop Introduction: Advances of AI Methods in Single Cell Spatial Omics.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
Same journal

DRIVE-KG: Enhancing variant-phenotype association discovery in understudied complex diseases using heterogeneous knowledge graphs.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
See all related articles

Related Experiment Video

Updated: Jun 18, 2026

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

RNA structural segmentation.

Ivan Dotú1, William A Lorenz, Pascal VAN Hentenryck

  • 1Department of Computer Science, Brown University, Box 1910, Providence, RI 02912, USA.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
|November 13, 2009
PubMed
Summary
This summary is machine-generated.

We developed dynamic programming algorithms to segment RNA structures into domains using base pairing, contact maps, or Voronoi tessellation. These methods accurately identify precursor microRNA boundaries and decompose large RNA structures.

More Related Videos

Substructure Analyzer: A User-Friendly Workflow for Rapid Exploration and Accurate Analysis of Cellular Bodies in Fluorescence Microscopy Images
14:28

Substructure Analyzer: A User-Friendly Workflow for Rapid Exploration and Accurate Analysis of Cellular Bodies in Fluorescence Microscopy Images

Published on: July 15, 2020

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

Related Experiment Videos

Last Updated: Jun 18, 2026

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Substructure Analyzer: A User-Friendly Workflow for Rapid Exploration and Accurate Analysis of Cellular Bodies in Fluorescence Microscopy Images
14:28

Substructure Analyzer: A User-Friendly Workflow for Rapid Exploration and Accurate Analysis of Cellular Bodies in Fluorescence Microscopy Images

Published on: July 15, 2020

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

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Structural Biology

Background:

  • RNA molecules fold into complex secondary and tertiary structures essential for their function.
  • Segmenting these structures into distinct domains aids in understanding their properties and biological roles.
  • Existing methods for RNA structure analysis can be computationally intensive and may not capture domain-level organization effectively.

Purpose of the Study:

  • To develop and evaluate dynamic programming algorithms for segmenting RNA secondary and tertiary structures into functional domains.
  • To apply these segmentation algorithms for precise identification of precursor microRNA boundaries.
  • To assess the utility of automated structural segmentation in decomposing large RNA molecules.

Main Methods:

  • Dynamic programming algorithms were designed for RNA structure segmentation.
  • Fitness functions incorporated base pairing probabilities, 3D structure contact maps, and Voronoi tessellation.
  • Novel algorithms included a parametric approach for k-class segmentation and simultaneous subsegment optimization.
  • Algorithms were tested on precursor microRNAs from the Rfam database and rRNA structures.

Main Results:

  • The developed segmentation algorithms accurately determined 5' and 3' boundaries of precursor microRNAs with high sensitivity (0.911) and positive predictive value (0.906).
  • Benchmarking showed low discrepancy in boundary prediction for precursor microRNAs.
  • Optimal structural segmentation effectively decomposed large RNA structures, such as rRNA, into distinct domains, aligning with manual segmentations.

Conclusions:

  • Dynamic programming-based structural segmentation provides an effective computational approach for analyzing RNA architecture.
  • These algorithms enhance the accuracy of identifying key RNA elements like precursor microRNAs.
  • Automated structural segmentation is a valuable tool for dissecting the complexity of large RNA molecules into manageable domains.