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-seq03:21

RNA-seq

12.3K
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...
12.3K
Conserved Binding Sites01:49

Conserved Binding Sites

5.2K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
5.2K
RNA Structure01:23

RNA Structure

79.7K
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...
79.7K
RNA Structure01:19

RNA Structure

8.0K
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...
8.0K
Nucleic Acid Structure01:25

Nucleic Acid Structure

9.7K
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...
9.7K
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

4.9K
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...
4.9K

You might also read

Related Articles

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

Sort by
Same author

Riboswitch-targeted improvement of lysine production in Bacillus and Priestia species.

NPJ science of food·2026
Same author

Characterization of the virus-host RNA-RNA interactome across important human pathogenic RNA viruses.

PLoS pathogens·2026
Same author

Exploring the regulatory potential of RNA structures in 202 cyanobacterial genomes.

Nucleic acids research·2026
Same author

CoMPaseD: advanced planning of proteomic experiments aiming to identify small proteins.

microLife·2026
Same author

Very high CO<sub>2</sub> concentrations inhibit photosynthesis and trigger transcriptomic stress responses in cyanobacteria.

NAR genomics and bioinformatics·2026
Same author

Associating cancer-related RNA structure disrupting SNPs in LincRNAs to function.

BMC genomics·2025

Related Experiment Video

Updated: Mar 5, 2026

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

5.3K

RNAscClust: clustering RNA sequences using structure conservation and graph based motifs.

Milad Miladi1, Alexander Junge2,3, Fabrizio Costa1

  • 1Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg im Breisgau, Germany.

Bioinformatics (Oxford, England)
|March 24, 2017
PubMed
Summary

RNAscClust accurately clusters paralogous RNA sequences by incorporating structural conservation and compensatory base pair changes. This method improves clustering accuracy by leveraging evolutionary information from orthologous sequences.

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

32.3K
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

16.1K

Related Experiment Videos

Last Updated: Mar 5, 2026

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

5.3K
RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

32.3K
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

16.1K

Area of Science:

  • Computational Biology
  • Bioinformatics
  • RNA Structure Analysis

Background:

  • Clustering RNA sequences by secondary structure aids RNA function studies.
  • Existing methods for clustering paralogous RNAs do not account for compensatory base pair changes from orthologous sequences.

Purpose of the Study:

  • To present RNAscClust, a novel algorithm for clustering structured RNAs that considers structural conservation.
  • To improve the accuracy of paralogous RNA clustering by integrating compensatory base pair changes.

Main Methods:

  • RNAscClust computes minimum free-energy structures using conserved base pairs as priors.
  • It clusters paralogous RNAs using a graph kernel-based strategy to identify common structural features.
  • The algorithm processes multiple structural alignments of RNA sequences.

Main Results:

  • Clustering accuracy significantly improves with a higher degree of compensatory base pair changes.
  • RNAscClust effectively groups paralogous RNAs based on conserved structural elements.
  • The method demonstrates the benefit of incorporating evolutionary structural information.

Conclusions:

  • RNAscClust offers an improved approach for clustering paralogous RNAs.
  • Accounting for compensatory base pair changes enhances the identification of structurally similar RNA families.
  • The algorithm provides a valuable tool for RNA functional genomics research.