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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Ribosome Profiling02:24

Ribosome Profiling

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.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

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Related Experiment Video

Updated: May 18, 2026

mRNA Interactome Capture from Plant Protoplasts
12:29

mRNA Interactome Capture from Plant Protoplasts

Published on: July 28, 2017

Site identification in high-throughput RNA-protein interaction data.

Philip J Uren1, Emad Bahrami-Samani, Suzanne C Burns

  • 1Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.

Bioinformatics (Oxford, England)
|October 2, 2012
PubMed
Summary
This summary is machine-generated.

A new computational method, Piranha, enhances RNA-binding protein site identification from CLIP and RIP-seq data. It accurately models read counts and incorporates external factors for improved analysis of gene regulation.

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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

Area of Science:

  • Molecular Biology
  • Computational Biology
  • Genomics

Background:

  • Post-transcriptional and co-transcriptional regulation are vital for linking genotype to phenotype.
  • RNA-binding proteins are key regulators, and technologies like CLIP and RIP-seq have advanced for their study.
  • Robust computational methods for identifying RNA-binding protein binding sites from high-throughput data are needed.

Purpose of the Study:

  • To develop a flexible and statistically robust computational method for RNA-binding protein site identification.
  • To address the limitations of existing methods in analyzing CLIP and RIP-seq data.
  • To enable accurate comparison of RNA-binding protein site usage across different conditions.

Main Methods:

  • Introduction of a novel computational method for binding site identification.
  • Implementation of the method in a software tool named Piranha.
  • Utilizing accurate modeling of read-count distributions and incorporating external covariates like transcript abundance.

Main Results:

  • The Piranha method is applicable to all variations of CLIP and RIP-seq technologies.
  • It accurately models underlying read-count distributions.
  • External covariates, such as transcript abundance, can inform the site identification process, and direct comparison of site usage across conditions is enabled.

Conclusions:

  • Piranha offers a significant advancement in RNA-binding protein binding site identification.
  • The tool provides a flexible and accurate approach for analyzing high-throughput immunoprecipitation assay data.
  • Freely available software facilitates broader adoption and research in gene regulation.