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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...
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Experimental RNAi02:15

Experimental RNAi

RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...

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Updated: May 17, 2026

Identification of Circular RNAs using RNA Sequencing
08:25

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

Multi-scale RNA comparison based on RNA triple vector curve representation.

Ying Li1, Ming Duan, Yanchun Liang

  • 1College of Computer Science and Technology, Symbol Computation and Knowledge Engineering Lab of Ministry of Education, Jilin University, Changchun, China.

BMC Bioinformatics
|November 1, 2012
PubMed
Summary
This summary is machine-generated.

We developed a new multi-scale RNA comparison method using RNA triple vector curves (TV-Curve) to analyze RNA sequence and structure. This approach effectively classifies non-coding RNAs and aids in RNA mutation analysis.

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Identification of Circular RNAs using RNA Sequencing
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10:10

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2

Published on: September 18, 2021

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • RNA molecules play crucial roles in biological processes, necessitating accurate methods for comparing their functions.
  • Traditional RNA similarity methods struggle with long-range correlations and often overlook structural features like base pairs.
  • Existing RNA comparison techniques are broadly categorized as alignment-based or alignment-free.

Purpose of the Study:

  • To develop a novel, structure-aware RNA similarity measure.
  • To enhance the understanding of functional relationships between RNAs.
  • To improve RNA classification and mutation analysis.

Main Methods:

  • Introduced a novel numerical representation of RNA secondary structure called RNA triple vectors curve (TV-Curve).
  • Developed a new similarity metric utilizing wavelet decomposition of the TV-Curve.
  • Applied the multi-scale RNA comparison method to non-coding RNA classification and RNA mutation analysis.

Main Results:

  • The proposed wavelet-based method, multi-scale RNA comparison, demonstrates potential in RNA classification and mutation analysis.
  • Comparison with established tools (RNAdistance, RNApdist) indicates the effectiveness of the new method.
  • The TV-Curve representation provides enhanced visualization and analysis, particularly for long RNAs.

Conclusions:

  • The TV-Curve tool offers a comprehensive characterization of both sequence and structure features in RNAs.
  • The multi-scale similarity measure effectively captures local and global differences in RNA sequence and structure.
  • The proposed method is validated as superior to existing approaches for non-coding RNA classification and RNA mutation analysis, revealing subtle RNA relationships.