  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.
