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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...
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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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RNA Interference

RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
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Related Experiment Video

Updated: Jun 18, 2026

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
10:52

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

Published on: September 28, 2017

Target prediction and a statistical sampling algorithm for RNA-RNA interaction.

Fenix W D Huang1, Jing Qin, Christian M Reidys

  • 1Center for Combinatorics, LPMC-TJKLC, Nankai University, Tianjin 300071, PR China.

Bioinformatics (Oxford, England)
|November 14, 2009
PubMed
Summary
This summary is machine-generated.

New dynamic programming algorithms enhance the study of RNA-RNA interactions, improving predictions for microRNA (miRNA) and small interfering RNA (siRNA) binding efficiency and specificity.

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Last Updated: Jun 18, 2026

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
10:52

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Published on: September 28, 2017

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A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA
13:00

A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA

Published on: December 2, 2009

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Molecular Biology

Background:

  • Target site accessibility critically influences RNA-RNA binding, affecting microRNA (miRNA) and small interfering RNA (siRNA) specificity and efficiency.
  • Recent advancements include dynamic programming (DP) algorithms with O(N(6)) time and O(N(4)) space complexity for RNA-RNA interaction complexes, offering thermodynamic insights.

Purpose of the Study:

  • To develop and implement novel algorithms for calculating RNA-RNA interaction probabilities.
  • To provide a method for computing 'hybrid probabilities' for specific RNA intervals.
  • To complement calculations with a stochastic sampling algorithm for Boltzmann-weighted structures.

Main Methods:

  • Modified grammars to enable calculation of interaction probabilities for target RNA intervals.
  • Development of a stochastic sampling algorithm to generate a Boltzmann weighted ensemble of RNA-RNA interaction structures.
  • Implementation of algorithms in C within the rip package.

Main Results:

  • Calculation of interaction probabilities for any given interval on the target RNA.
  • Generation of a Boltzmann weighted ensemble of RNA-RNA interaction structures using stochastic sampling.
  • Sampling of k structures with negligible additional memory and O(k.N(3)) runtime.

Conclusions:

  • The developed algorithms and software package (rip2) provide enhanced capabilities for analyzing RNA-RNA interactions.
  • These tools offer detailed insights into thermodynamic properties and binding probabilities, crucial for understanding miRNA and siRNA function.
  • The rip2 package is publicly available for download, facilitating further research in the field.