GMOL: An Interactive Tool for 3D Genome Structure Visualization

TL;DR

GMOL is an interactive desktop tool that enables multi-scale visualization and analysis of 3D genome structures, aiding researchers in understanding genome architecture and its functional implications.

Contribution

The paper introduces GMOL, a novel multi-scale visualization tool for genome structures, including a new file format GSS and features for measurement and data extraction.

Findings

Supports visualization at six genome scales

Allows retrieval of genome sequences from Ensembl or local databases

Enables measurement and static image export of genome structures

Abstract

It has been shown that genome spatial structures largely affect both genome activity and DNA function. Knowing this, many researchers are currently attempting to accurately model genome structures. Despite these increased efforts there still exists a shortage of tools dedicated to visualizing the genome. Creating a tool that can accurately visualize the genome can aid researchers by highlighting structural relationships that may not be obvious when examining the sequence information alone. Here we present a desktop application, known as GMOL, designed to effectively visualize genome tertiary structures at multiple scales so that researchers may better analyze their genomic data. GMOL was developed based upon our multi-scale approach that allows a user to zoom in and out between six separate levels within the genome. These six scales are full genome, chromosome, loci, fiber, nucleosome, and nucleotide. In order to store the data of the different scales, a new file format, known as GSS, was created. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences from either Ensembl or a local database. Users can also interactively manipulate and measure the whole genome structure and extract static images and machine-readable data files in PDB format from the multi-scale structure. By using GMOL researchers will be able to better understand and analyze genome structure models and the impact their structural relations have on genome activity and DNA function through GMOLs unique features and functions, which includes the multi-scale method that can satisfy the users requirement to not only visualize genome tertiary structure, but also measure it.