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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 Structure01:23

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...
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...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Protein Organization01:13

Protein Organization

Overview

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Related Experiment Video

Updated: Jul 19, 2026

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Pure multiple RNA secondary structure alignments: a progressive profile approach.

Matthias Höchsmann1, Björn Voss, Robert Giegerich

  • 1International Graduate School in Bioinformatics and Genome Research, University of Bielefeld, Bielefeld, Germany. mhoechsm@techfak.uni-bielefeld.de

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|October 20, 2006
PubMed
Summary

This study introduces a novel method for aligning RNA secondary structures using a tree alignment model. This approach enables clustering RNA molecules based on structural similarity, independent of sequence.

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Published on: September 21, 2017

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Molecular Biology

Background:

  • Noncoding RNA function is intrinsically linked to its structure.
  • Predicting 2D RNA structure offers insights into 3D conformations and is crucial for inferring function.
  • Structure comparison is key to understanding functional relationships between RNA molecules.

Purpose of the Study:

  • To develop a method for multiple RNA secondary structure alignments.
  • To enable RNA clustering based solely on structural features, bypassing sequence similarity requirements.
  • To introduce a generalized profile alignment method for trees and forests.

Main Methods:

  • Utilizing a tree alignment model for multiple RNA secondary structure alignments.
  • Generalizing the profile alignment method from strings to trees and forests.
  • Introducing a tree profile representation for RNA secondary structure alignments.

Main Results:

  • A method for computing multiple RNA secondary structure alignments was established.
  • A tree profile representation was introduced for effective RNA structure comparison and scoring.
  • The RNA profile serves as a data structure for representing multiple RNA structures.

Conclusions:

  • The developed method allows for structural-based clustering of RNA molecules.
  • The RNA profile representation is valuable for comparative analysis and data management of RNA structures.
  • A visualization of consensus RNA structures, incorporating sequence information, was proposed.