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

RNA-seq

RNA-seq

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...

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...

You might also read

Related Articles

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

Sort by

Same author

Navigation of Nanos germ cell specification factor to germ granules-posttranscriptional regulation hubs-across species†.

Biology of reproduction·2026

Same author

Isoform-Specific Localization Diversifies Human MSI2 Function.

bioRxiv : the preprint server for biology·2026

Same author

Extremely High Excitonic g Factors in 2D Crystals by Alloy-Induced Admixing of Band States.

Physical review letters·2026

Same author

The NANOS RNA-binding protein variants: a model for understanding human infertility.

Journal of applied genetics·2025

Same author

Nanopore sequencing of intact aminoacylated tRNAs.

Nature communications·2025

Same author

Navigation of Nanos germ cell specification factor to germ granules-posttranscriptional regulation hubs-across species†.

Biology of reproduction·2025

Search research articles

Related Experiment Video

Updated: Oct 16, 2025

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

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

Published on: December 9, 2022

RNAlign2D: a rapid method for combined RNA structure and sequence-based alignment using a pseudo-amino acid

Tomasz Woźniak¹, Małgorzata Sajek², Jadwiga Jaruzelska¹

¹Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479, Poznań, Poland.

BMC Bioinformatics

|October 17, 2021

Summary

RNAlign2D is a new Python tool that rapidly aligns multiple RNA sequences using pseudo-amino acid sequences. This bioinformatics approach significantly speeds up RNA classification and function discovery.

Keywords:

RNA RNA 2D structure RNA alignment RNA secondary structure alignment Structure alignment

More Related Videos

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

Published on: July 10, 2020

Related Experiment Videos

Last Updated: Oct 16, 2025

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

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

Published on: December 9, 2022

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

Published on: July 10, 2020

Area of Science:

Bioinformatics
Computational Biology
RNA Structure and Function

Background:

RNA secondary structures dictate molecular functions.
Bioinformatic tools predict RNA functions via multiple RNA alignment.
Existing tools are slow for long or numerous RNA sequences.

Purpose of the Study:

To develop a faster multiple RNA alignment tool.
To improve RNA classification and functional analysis.
To aid in the discovery of functions for novel RNAs.

Main Methods:

Introduction of RNAlign2D, a Python-based tool.
Conversion of RNA sequences into pseudo-amino acid sequences incorporating structural information.
Alignment of RNA molecules using the MUSCLE tool with a customizable scoring matrix.

Main Results:

RNAlign2D achieves extremely fast RNA alignments.
The tool produces accurate RNA alignments.
Demonstrates significant speed improvement over existing methods.

Conclusions:

RNAlign2D offers accurate and rapid multiple RNA alignment.
The pseudo-amino acid substitution matrix method is versatile.
This approach is compatible with most protein alignment tools.