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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...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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...
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...

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Related Experiment Video

Updated: Jun 6, 2026

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

On comparing two structured RNA multiple alignments.

Vandanaben Patel1, Jason T L Wang, Shefali Setia

  • 1Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102, USA. vgp22@njit.edu

Journal of Bioinformatics and Computational Biology
|December 2, 2010
PubMed
Summary
This summary is machine-generated.

BlockMatch aligns RNA blocks by considering sequences and consensus structures for high-quality results. This RNA alignment method improves phylogenetic tree accuracy compared to existing tools.

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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
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RNA Secondary Structure Prediction Using High-throughput SHAPE
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RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Related Experiment Videos

Last Updated: Jun 6, 2026

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
09:37

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

Published on: August 15, 2019

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • RNA sequences and their secondary structures are crucial for biological function.
  • Accurate multiple sequence alignment is essential for understanding RNA evolution and function.
  • Existing tools often align sequences or structures independently, limiting alignment quality.

Purpose of the Study:

  • To introduce BlockMatch, a novel method for aligning RNA blocks.
  • To improve the accuracy of RNA multiple sequence alignment by integrating sequence and structure information.
  • To enhance phylogenetic reconstruction using accurate RNA alignments.

Main Methods:

  • BlockMatch utilizes a quadratic-time dynamic programming algorithm.
  • It aligns columns and column pairs within RNA blocks, considering all sequences and consensus structures.
  • The method processes RNA alignments in Stockholm format.

Main Results:

  • BlockMatch achieved high-quality RNA alignment results.
  • Phylogenetic tree reconstruction using BlockMatch on 5S rRNA bacterial sequences was more accurate than using ClustalW.
  • The method effectively integrates sequence and structural information for alignment.

Conclusions:

  • BlockMatch offers a superior approach for aligning RNA blocks, especially for phylogenetic analysis.
  • The integration of sequence and consensus secondary structure information is key to improved alignment accuracy.
  • BlockMatch provides a valuable tool for bioinformatics research, with a web server and downloadable software available.