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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...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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...

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Related Experiment Video

Updated: Jun 2, 2026

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars.

Zsuzsanna Sükösd1, Bjarne Knudsen, Morten Vaerum

  • 1Interdisciplinary Nanoscience Center, Aarhus University, Denmark. zs@mb.au.dk

BMC Bioinformatics
|April 20, 2011
PubMed
Summary

PPfold is a new parallelized algorithm that accurately predicts large RNA structures quickly. It overcomes limitations of previous models, enabling efficient analysis of genomic sequences.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • RNA Structure Prediction

Background:

  • Predicting large RNA structures is computationally challenging for existing algorithms.
  • The pfold model offers high accuracy but suffers from time complexity and underflow errors, limiting its use for long RNA sequences.

Purpose of the Study:

  • To present PPfold, a multithreaded version of the pfold model.
  • To enable accurate and efficient prediction of large RNA secondary structures on practical timescales.

Main Methods:

  • PPfold parallelizes phylogenetic calculations and the inside-outside algorithm for reduced runtime on multicore systems.
  • Implements an extended-exponent datatype to resolve floating-point underflow issues inherent in the pfold model.
  • Enhances user interface and portability, offering standalone executables, Java source code, and a CLC Workbenches plugin.

Main Results:

  • PPfold significantly reduces runtime for RNA structure prediction on multicore machines.
  • Successfully predicted the secondary structure of 24 complete HIV-1 genomes in 65 minutes on an 8-core machine.
  • Identified known structural elements within the HIV-1 genome prediction, demonstrating practical utility.

Conclusions:

  • PPfold is the first parallelized comparative RNA structure prediction algorithm.
  • Provides fast, high-quality predictions for large RNA secondary structures, including viral genomes and long transcripts.
  • The parallelization techniques employed may have broader applications in bioinformatics.