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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...
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 13, 2026

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing (RIPiT-Seq)
09:26

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing (RIPiT-Seq)

Published on: July 10, 2019

RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments.

Yue Li1, Dorothy Yanling Zhao, Jack F Greenblatt

  • 1Department of Computer Science, University of Toronto, Toronto, Ontario M5S 2E4, Canada.

Nucleic Acids Research
|March 5, 2013
PubMed
Summary
This summary is machine-generated.

RIPSeeker is a new R package for analyzing RNA-binding protein immunoprecipitation sequencing (RIP-seq) data. It offers superior accuracy in identifying RNA-protein interactions compared to existing methods.

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Related Experiment Videos

Last Updated: May 13, 2026

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing (RIPiT-Seq)
09:26

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing (RIPiT-Seq)

Published on: July 10, 2019

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
05:07

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • RNA-binding protein immunoprecipitation sequencing (RIP-seq) identifies genome-wide RNA transcripts interacting with proteins.
  • Existing RIP-seq analysis lacks dedicated statistical tools, presenting unique challenges.
  • RNA-protein interaction studies are crucial for understanding gene regulation.

Purpose of the Study:

  • To develop and validate a novel statistical tool for de novo RIP-seq peak prediction.
  • To provide a comprehensive bioinformatics package for RIP-seq data analysis.

Main Methods:

  • Development of RIPSeeker, an open-source Bioconductor/R package utilizing a Hidden Markov Model (HMM).
  • Comparative analysis of RIPSeeker against six other programs using three RIP-seq and two PAR-CLIP datasets.
  • Evaluation using receiver operating characteristic (ROC) curves to assess sensitivity and specificity.

Main Results:

  • RIPSeeker demonstrated superior sensitivity and specificity in identifying high-confidence RIP-seq peaks.
  • The package dominated 9 out of 12 evaluation metrics, achieving an average 80% area under the curve.
  • RIPSeeker-identified peaks were enriched for biologically relevant genomic elements, motifs, and known RNA-protein interactions.

Conclusions:

  • RIPSeeker is a highly effective tool for RIP-seq data analysis, outperforming existing methods.
  • The package offers integrated bioinformatics tools for comprehensive RIP-seq data processing, visualization, and annotation.
  • RIPSeeker advances the study of RNA-protein interactions and gene regulation.