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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...
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...
Protein Organization01:13

Protein Organization

Overview

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Related Experiment Video

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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Predicting the secondary structure common to two RNA sequences with Dynalign.

David Mathews1

  • 1Center for Human Genetics and Molecular Pediatric Disease Aab Institute of Biomedical Sciences University of Rochester Medical Center, Rochester, New York, USA.

Current Protocols in Bioinformatics
|April 23, 2008
PubMed
Summary

Dynalign, a dynamic programming algorithm, improves RNA secondary structure prediction accuracy by analyzing two sequences simultaneously. Protocols are provided for its use on Windows and Unix/Linux systems.

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Area of Science:

  • Computational biology
  • Bioinformatics
  • Molecular biology

Background:

  • Accurate prediction of RNA secondary structure is crucial for understanding RNA function.
  • Existing methods often focus on single sequences, potentially limiting accuracy for related RNAs.
  • Dynamic programming offers a robust framework for sequence analysis.

Purpose of the Study:

  • To introduce Dynalign, a dynamic programming algorithm for simultaneous RNA secondary structure prediction and sequence alignment.
  • To demonstrate the improved accuracy of Dynalign compared to single-sequence free-energy minimization.
  • To provide practical protocols for implementing Dynalign on different computing platforms.

Main Methods:

  • Utilizing dynamic programming for simultaneous prediction of common secondary structure and alignment of two RNA sequences.
  • Comparing Dynalign's prediction accuracy against traditional single-sequence free-energy minimization methods.
  • Developing and documenting protocols for Dynalign execution on Microsoft Windows (RNAstructure package) and Unix/Linux environments.

Main Results:

  • Dynalign achieves higher average accuracy in secondary structure prediction compared to single-sequence methods.
  • The algorithm successfully predicts common secondary structures for pairs of RNA sequences.
  • Protocols facilitate the application of Dynalign in both Windows and Unix/Linux operating systems.

Conclusions:

  • Dynalign offers a significant advancement in predicting RNA secondary structures for related sequences.
  • The simultaneous prediction and alignment approach enhances overall accuracy.
  • User-friendly protocols ensure broader accessibility and application of Dynalign in RNA research.