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Related Concept Videos

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...
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 Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...

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RNA secondary structure analysis using the Vienna RNA package.

Ivo L Hofacker1

  • 1University of Vienna-Institute of Theoretical Chemistry, Vienna, Austria.

Current Protocols in Bioinformatics
|June 5, 2009
PubMed
Summary

This guide explains the Vienna RNA package for analyzing RNA secondary structures. It covers predicting structures, RNA-RNA interactions, and designing RNA sequences.

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Molecular Biology

Background:

  • RNA molecules play crucial roles in various biological processes.
  • Understanding RNA secondary structure is essential for deciphering RNA function.
  • Accurate prediction of RNA structures is a fundamental challenge in molecular biology.

Purpose of the Study:

  • To provide a comprehensive guide on utilizing the Vienna RNA package.
  • To demonstrate the package's capabilities for diverse RNA structure analysis tasks.
  • To facilitate researchers' work in RNA bioinformatics and molecular design.

Main Methods:

  • Utilizing the Vienna RNA package for computational analysis.
  • Applying algorithms for RNA secondary structure prediction.

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  • Implementing methods for predicting consensus structures and RNA-RNA interactions.
  • Employing sequence design functionalities within the package.

    • Main Results:

    • The Vienna RNA package offers robust tools for RNA secondary structure analysis.
    • The package supports prediction for single sequences and consensus structures.
    • It enables the analysis of RNA-RNA interactions and facilitates RNA sequence design.

    Conclusions:

    • The Vienna RNA package is a valuable resource for researchers in RNA biology.
    • Effective use of the package aids in understanding RNA structure-function relationships.
    • The documented functionalities streamline complex RNA analysis and design workflows.