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RNA-seq

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...

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Updated: Oct 14, 2025

3' End Sequencing Library Preparation with A-seq2

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

Peakhood: individual site context extraction for CLIP-seq peak regions.

Michael Uhl¹, Dominik Rabsch¹, Florian Eggenhofer¹

¹Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg im Breisgau, Germany.

Bioinformatics (Oxford, England)

|November 4, 2021

Summary

Peakhood is a new tool that assigns RNA-binding protein (RBP) binding sites to specific RNA contexts, improving analysis of CLIP-seq data. It accurately models RBP binding behavior on spliced RNA transcripts.

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PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

Area of Science:

Molecular Biology
Bioinformatics
Genomics

Background:

RNA-binding proteins (RBPs) are crucial for gene regulation.
CLIP-seq is the standard method for mapping RBP binding sites genome-wide.
Existing peak callers analyze genomic context, but many RBPs bind to spliced RNA contexts.

Purpose of the Study:

To develop a tool for assigning CLIP-seq peak regions to specific RNA contexts.
To accurately model RBP binding behavior on spliced transcripts.
To identify splice variants for transcript-context binding sites.

Main Methods:

Peakhood utilizes CLIP-seq peak regions, read data, and genomic annotations.
It assigns individual context (genomic or transcript) to each peak region.
For transcript-context sites, it identifies the most likely splice variant.

Main Results:

Peakhood is the first tool to assign individual context to CLIP-seq peak regions.
It accurately determines splice variants for transcript-context binding sites.
The tool merges results from multiple datasets for comprehensive analysis.

Conclusions:

Peakhood enables precise mapping of RBP binding sites to RNA contexts.
This improves the understanding of RBP function in gene regulation.
The tool facilitates comprehensive analysis of transcript-context binding sites.