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Related Concept Videos

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

Published on: December 9, 2022

Interval-based distance function for identifying RNA structure candidates.

Qingfeng Chen1, Gang Li, Yi-Ping Phoebe Chen

  • 1School of Computer, Electronic and Information, Guangxi University, Nanning 530004, China. qingfeng@gxu.edu.cn

Journal of Theoretical Biology
|November 9, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces a novel Hausdorff distance measure for clustering RNA secondary structures, addressing challenges posed by complex biological data. The new method accurately computes similarity between RNA structures, improving biological data analysis.

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Last Updated: Jun 6, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

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Published on: December 9, 2022

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

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Published on: May 31, 2013

Identification of Circular RNAs using RNA Sequencing
08:25

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Traditional clustering algorithms face challenges in analyzing complex RNA secondary structures.
  • Existing distance measures in high-dimensional space often overlook data correlations, focusing only on scale.

Purpose of the Study:

  • To develop a novel interval-based distance measure for RNA structure data analysis.
  • To enhance the similarity computation for characterized RNA structures, considering complex relationships.

Main Methods:

  • A novel interval-based Hausdorff distance measure was developed.
  • The measure considers three types of relationships: perfect match, partially overlapped, and non-overlapped structures.
  • The method was applied to a dataset of RNA secondary structures from the Rfam database.

Main Results:

  • The developed Hausdorff distance measure effectively computes similarity between RNA secondary structures.
  • The method demonstrates applicability in analyzing biological data with complex structures.
  • The approach addresses limitations of traditional distance measures by incorporating correlation aspects.

Conclusions:

  • The novel Hausdorff distance measure offers a robust approach for clustering RNA secondary structures.
  • This method advances RNA structure data analysis by providing a more accurate similarity computation.
  • The findings contribute to improved clustering techniques in bioinformatics and computational biology.