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

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 Stability01:53

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
RNA Stability01:53

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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...

You might also read

Related Articles

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

Sort by
Same author

Ancestral protein sequence reconstruction using a tree-structured Ornstein-Uhlenbeck variational autoencoder.

... International Conference on Learning Representations·2026
Same author

An almost infinite sites model.

Theoretical population biology·2024
Same author

Comparing Phylogeographies to Reveal Incompatible Geographical Histories within Genomes.

Molecular biology and evolution·2024
Same author

Recoverability of ancestral recombination graph topologies.

Theoretical population biology·2023
Same author

Cable bacteria with electric connection to oxygen attract flocks of diverse bacteria.

Nature communications·2023
Same author

The impact of COVID-19 certification mandates on the number of cases of and hospitalizations with COVID-19 in the UK: A difference-in-differences analysis.

Frontiers in public health·2023

Related Experiment Video

Updated: May 22, 2026

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Evolving stochastic context--free grammars for RNA secondary structure prediction.

James Wj Anderson, Paula Tataru, Joe Staines

    BMC Bioinformatics
    |May 8, 2012
    PubMed
    Summary

    Automatic search techniques for Stochastic Context-Free Grammars (SCFGs) effectively identified new RNA secondary structure prediction models. Many found grammars, including ambiguous ones, showed predictive accuracy comparable to manually designed models.

    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

    Related Experiment Videos

    Last Updated: May 22, 2026

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

    RNA Secondary Structure Prediction Using High-throughput SHAPE

    Published on: May 31, 2013

    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
    • Genomics

    Background:

    • Stochastic Context-Free Grammars (SCFGs) have been foundational in RNA secondary structure prediction since the 1990s.
    • Dominant SCFGs for RNA structure prediction were intuitively designed, despite a vast potential search space.
    • Previous assumptions suggested grammar ambiguity might hinder RNA structure prediction accuracy.

    Purpose of the Study:

    • To investigate automatic search techniques for discovering effective SCFGs for RNA secondary structure prediction.
    • To compare the performance of exhaustively searched compact grammars and evolutionarily derived larger grammars.
    • To evaluate the impact of grammar ambiguity on RNA structure prediction efficacy.

    Main Methods:

    • Employed exhaustive search to identify compact SCFGs.
    • Utilized an evolutionary algorithm to discover larger, potentially more complex SCFGs.
    • Applied these search techniques to a comprehensive dataset for RNA secondary structure prediction.

    Main Results:

    • Automatic search yielded novel SCFGs for RNA secondary structure prediction, though none significantly outperformed established models.
    • Diverse SCFG structures demonstrated comparable predictive abilities.
    • Numerous ambiguous grammars exhibited predictive accuracy on par with or exceeding the best unambiguous grammars.

    Conclusions:

    • Evolving SCFGs is an effective strategy for discovering RNA secondary structure prediction models with high accuracy.
    • The predictive performance of automatically generated grammars matched or surpassed manually designed ones.
    • Ambiguous grammars are viable and effective tools for RNA secondary structure prediction, challenging prior assumptions.