Biological Arc Diagrams

Biological Arc Diagrams (BARD) was developed as part of my PhD research that investigated the use of information visualization in comparative genomic analysis. BARD is an information visualization software tool for visualizing the repetitive structures in biological sequences. The goal of the project is to provide a visual metaphor to aid biological feature discovery in comparative genomics. The salient biological features are rendered as interesting geometric patterns. The software is based on the Arc Diagram algorithm developed by Martin Wattenburg.

The following image shows the matching genes on the forward and reverse DNA strands within the mating region of 6 strains of Cryptococcus neoformans.
figure 1

This image is a filtered and shaded view of the image above. It depicts a story of evolutionary biology within this region. The arcs connecting the regions on the right are more visually organized than those on the left. This is a visual artifact that reflects biological pressure to conserve the gene order within regions that are biologically significant for the organism. The preserved gene order, synteny, of the sequences on the right corresponds to the human pathogenic strains of the organism. This picture illustrates nature’s tendency to preserve the pathogenic functionality of these strains as compared to their related cousins on the left.

figure 2