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Updated: Dec 26, 2025

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework.

Martin Lewinski¹, Yannik Bramkamp², Tino Köster²

¹RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Universitaetsstrasse 25, Bielefeld, Germany. martin.lewinski@uni-bielefeld.de.

BMC Bioinformatics

|March 19, 2020

Summary

This summary is machine-generated.

SEQing is a new, accessible dashboard for visualizing RNA-binding protein (RBP) interactions identified by individual nucleotide resolution crosslinking immunoprecipitation (iCLIP). This tool aids in understanding RBP function by cross-referencing binding sites with gene expression data.

Keywords:

Alternative splicing Binding sites Data safety Genomic tracks Interactive visualization Python RNA-Seq RNA-binding protein Web-based iCLIP

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Published on: July 16, 2017

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

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Published on: April 30, 2011

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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

Area of Science:

Molecular Biology
Bioinformatics
Genomics

Background:

RNA-binding proteins (RBPs) are crucial regulators of gene expression.
Identifying RBP binding sites genome-wide is essential for understanding their function.
Individual nucleotide resolution crosslinking immunoprecipitation (iCLIP) is a key technique for mapping RBP binding sites.

Purpose of the Study:

To develop a user-friendly and secure tool for visualizing iCLIP data.
To enable cross-referencing of RBP binding data with other relevant biological datasets.
To facilitate collaborative analysis and data sharing among researchers.

Main Methods:

Development of SEQing, a customizable, interactive web-based dashboard.
Implementation of features for visualizing iCLIP crosslink sites on target genes.
Integration of RNA-sequencing (RNA-seq) data visualization in a separate tab.
Inclusion of a feature to display detailed target gene information.

Main Results:

SEQing provides an accessible platform for visualizing iCLIP data.
The dashboard allows for integrated analysis of iCLIP and RNA-seq data.
This integration aids in inferring the functional relevance of RBP binding sites.
SEQing supports secure, password-protected data sharing for collaboration.

Conclusions:

SEQing offers a versatile solution for iCLIP data visualization and analysis.
The tool enhances accessibility through web-based and mobile device compatibility.
Its customizable nature and security features make it valuable for research collaborations.
The source code is publicly available, promoting open science practices.