Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

Protein Folding Quality Check in the RER

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 Structure

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 Structure

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...

Nucleic Acid Structure

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...

Multi-species Conserved Sequences

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...

You might also read

Related Articles

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

Sort by

Same author

Treeline Provides a Unified Strategy for Optimising Phylogenetic Trees Under Alternative Criteria.

Molecular ecology resources·2026

Same author

Accurate detection of tandem repeats exposes ubiquitous reuse of biological sequences.

Nucleic acids research·2025

Same author

EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals.

Nature communications·2025

Same author

Tandem Repeats Provide Evidence for Convergent Evolution to Similar Protein Structures.

Genome biology and evolution·2025

Same author

Vancomycin-resistant Staphylococcus aureus (VRSA) can overcome the cost of antibiotic resistance and may threaten vancomycin's clinical durability.

PLoS pathogens·2024

Same author

Applications of Machine Learning on Electronic Health Record Data to Combat Antibiotic Resistance.

The Journal of infectious diseases·2024

Same journal

Optimized tRNA structure-seq reveals robust tRNA secondary structures in <i>S. cerevisiae</i> under mild stress conditions.

RNA (New York, N.Y.)·2026

Same journal

SERIPH: A Two-Step Extraction Protocol for Selective Enrichment of Semi-Extractable RNAs.

RNA (New York, N.Y.)·2026

Same journal

Reduced Sensitivity to RNA Structural Differences Distinguishes Eukaryotic Pus4 from Bacterial TruB.

RNA (New York, N.Y.)·2026

Same journal

Puf3 contributes to changes in mRNA solubility, translation elongation dynamics at rare arginine codons and loss of protein homeostasis in cells lacking Not4.

RNA (New York, N.Y.)·2026

Same journal

RBM38 Regulates HORMAD1 Splicing to Enhances MEK Inhibitor Sensitivity in Breast Cancer.

RNA (New York, N.Y.)·2026

Same journal

EF-P Inhibits Ribosomal α-Hydroxy Acid Incorporation: Strategic tRNA Body Selection for Co-incorporating α-Hydroxy Acids and Nonproteinogenic Amino Acids into Depsipeptides.

RNA (New York, N.Y.)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Dec 29, 2025

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency.

Erik S Wright¹

¹Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania 15219, USA.

RNA (New York, N.Y.)

|February 2, 2020

Summary

This summary is machine-generated.

A new benchmark, RNAconTest, evaluates RNA alignment tools by assessing conserved secondary structures. It reveals DAFS, DECIPHER, LocARNA, and MAFFT as top performers for structurally consistent alignments.

Keywords:

benchmark consensus secondary structure multiple sequence alignment noncoding RNA secondary structure prediction

More Related Videos

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

Related Experiment Videos

Last Updated: Dec 29, 2025

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Noncoding RNA importance is growing, necessitating effective comparative analysis tools.
Current benchmarks for RNA alignment and secondary structure prediction are limited in scope and sequence diversity.
Comparative methods rely on multiple sequence alignments to detect and analyze new RNA families.

Purpose of the Study:

To introduce RNAconTest, a novel benchmarking approach for evaluating RNA alignment and secondary structure prediction tools.
To assess the performance of popular alignment programs using a more robust and diverse benchmark.
To identify the most effective tools for comparative RNA sequence analysis.

Main Methods:

RNAconTest scores alignments based on the consistency of known secondary structures within reference sequences.
Consensus secondary structure predictions are evaluated for agreement with known family structures.
Ten popular alignment programs were compared using the RNAconTest benchmark.

Main Results:

DAFS, DECIPHER, LocARNA, and MAFFT produced the most structurally consistent alignments.
DAFS and LocARNA (with RNAalifold) generated the best consensus secondary structure predictions.
Many noncoding RNA-specific methods showed poor scalability with increasing sequence number or length.

Conclusions:

RNAconTest offers a valuable method for testing and improving tools for comparative RNA analysis.
The study highlights DAFS, DECIPHER, LocARNA, and MAFFT as leading tools for RNA alignment and structure prediction.
Current tools face challenges with scalability and performance degradation on larger datasets.