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Related Experiment Video

Updated: Feb 16, 2026

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

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

Published on: July 16, 2017

Delta: a new web-based 3D genome visualization and analysis platform.

Bixia Tang^1,2,3, Feifei Li¹, Jing Li¹

¹CAS Key Laboratory of Genome Sciences and Information, Chinese Academy of Sciences, Beijing 101300, China.

Bioinformatics (Oxford, England)

|December 19, 2017

Summary

This summary is machine-generated.

Delta visualizes genome architecture, predicting topologically associating domains and chromatin loops from Hi-C data. This platform aids in exploring 3D genome structure and generating hypotheses for biological insights.

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Area of Science:

Genomics
Computational Biology
Bioinformatics

Background:

Understanding the 3D physical architecture of the genome is crucial for deciphering gene regulation.
Existing tools often lack integrated visualization and analysis capabilities for 3D genome structures.

Purpose of the Study:

To develop an integrative platform, Delta, for visualizing and analyzing the 3D physical architecture of genomes.
To facilitate the prediction of topologically associating domains and chromatin loops.
To enable hypothesis generation and testing through integrated visualization of 3D genome models and annotations.

Main Methods:

Delta accepts Hi-C or ChIA-PET contact matrices as input.
It predicts topologically associating domains and chromatin loops.
Generates a consensus 3D genome model and provides an interactive visualization tool.

Main Results:

Delta successfully generates plausible 3D genome models.
The platform integrates 3D structure with extensive genome annotations.
A case study on the β-globin gene locus demonstrated intuitive hypothesis testing.

Conclusions:

Delta is a powerful tool for exploring and annotating the 3D genome.
The platform facilitates the integration of genome topology with functional genomics data.
Delta enables visual hypothesis generation and testing for biological mechanisms.