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Related Concept Videos

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 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-seq03:21

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 microarray-based...
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...

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Related Experiment Video

Updated: May 20, 2026

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

A method for discovering common patterns from two RNA secondary structures and its application to structural repeat

Lei Hua1, Jason T L Wang, Xiang Ji

  • 1Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey 07102, USA. lh56@njit.edu

Journal of Bioinformatics and Computational Biology
|July 20, 2012
PubMed
Summary
This summary is machine-generated.

DiscoverR identifies common patterns in RNA secondary structures using tree pattern discovery. This method finds the largest shared substructures and repeated regions within RNA molecules, aiding biological analysis.

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RNA Secondary Structure Prediction Using High-throughput SHAPE
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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Area of Science:

  • Bioinformatics
  • Computational Biology
  • RNA Structure Analysis

Background:

  • RNA secondary structures are crucial for gene regulation and function.
  • Identifying common patterns and repeats in RNA is essential for understanding structure-function relationships.
  • Existing methods may lack efficiency or the ability to find complex substructures.

Purpose of the Study:

  • To introduce DiscoverR, an ab initio method for identifying common patterns between two RNA secondary structures.
  • To extend DiscoverR for detecting repeated regions within a single RNA secondary structure.
  • To demonstrate the biological relevance of DiscoverR's findings through an application in gene analysis.

Main Methods:

  • Representing RNA secondary structures as ordered labeled trees.
  • Employing an efficient dynamic programming algorithm for tree pattern discovery.
  • Applying the extended method to find structural repeats in the 3'-untranslated region of a protein kinase gene.

Main Results:

  • DiscoverR successfully identifies and extracts the largest common substructures from RNA molecules of varying sizes.
  • The extended method detected significant structural repeats in the 3'-untranslated region of a protein kinase gene.
  • A biologically significant repeated hairpin was identified, showcasing the method's utility.

Conclusions:

  • DiscoverR provides an effective approach for comparative analysis of RNA secondary structures.
  • The method facilitates the discovery of biologically relevant structural motifs and repeats.
  • DiscoverR is a valuable tool for RNA bioinformatics research.