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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...
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...
Nucleic Acids02:43

Nucleic Acids

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the...
Nucleic acids02:43

Nucleic acids

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
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...

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Related Experiment Video

Updated: Jun 6, 2026

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

RNA-RNA interaction prediction based on multiple sequence alignments.

Andrew X Li1, Manja Marz, Jing Qin

  • 1Tianjin Key Laboratory of Combinatorics, Nankai University Tianjin 300071, People's Republic of China.

Bioinformatics (Oxford, England)
|December 8, 2010
PubMed
Summary
This summary is machine-generated.

Ripalign enhances RNA-RNA interaction structure prediction by integrating evolutionary information from multiple sequence alignments (MSA). This method improves sensitivity and specificity over previous algorithms by considering both thermodynamic stability and sequence/structure covariation.

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Last Updated: Jun 6, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE
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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Molecular Biology

Background:

  • Existing RNA-RNA interaction structure prediction methods often neglect evolutionary information.
  • Dynamic programming algorithms for RNA-RNA interaction complexes have O(N(6)) time and O(N(4)) space complexity.
  • Integrating thermodynamic stability with sequence/structure covariation is crucial for accurate structure determination.

Purpose of the Study:

  • To develop a novel algorithm, ripalign, for RNA-RNA interaction structure prediction.
  • To incorporate evolutionary information from multiple sequence alignments (MSA) into the prediction process.
  • To improve the accuracy and efficiency of RNA-RNA interaction structure prediction.

Main Methods:

  • The ripalign algorithm takes two multiple sequence alignments (MSA) as input.
  • It computes the partition function, base pairing probabilities, and hybrid probabilities.
  • It generates Boltzmann-sampled suboptimal structures compatible with the given alignments.

Main Results:

  • Ripalign offers significantly improved sensitivity and specificity compared to the single sequence-pair folding algorithm rip.
  • The algorithm requires negligible additional memory resources compared to rip.
  • Ripalign can incorporate structure constraints as input parameters.

Conclusions:

  • Ripalign effectively integrates evolutionary information from MSAs for enhanced RNA-RNA interaction structure prediction.
  • The algorithm provides a valuable tool for researchers studying RNA-RNA interactions.
  • Ripalign represents a significant advancement in computational approaches to RNA structure prediction.