Introductory Video on how to install the Visual genome Browser

 For the best experience this need to be viewed on a 4K screen.

While exploring genome data provided by the University of Santa Cruz, I developed a concept to visualize the human genome in a two-dimensional space. As a programmer, I wanted to gain a better understanding of the digital data contained within the genome, which codes for protein machines such as enzymes and structural and control proteins like transcription factors, enhancers, and suppressors. However, the standard linear axis representation did not provide sufficient insight into the genome's structure, particularly the repetitive patterns in regions like the centromeres and telomeres of chromosomes.

Drawing on my experience in GIS, I sought to represent large amounts of map data in two dimensions with multiple layers of information overlaid on top of each other. Applying the same approach to the genome, I aimed to depict the chromosomes as compactly as possible by using coloured blocks running from left to right and top to bottom. By adjusting the line width, any repetitive patterns in the data could become visible.

To achieve this, I decided to use the GC content as a metric and map it onto an RGB colour scale, with green reminding me of GFP, which is often used in fluorescent reporter assays. I discovered that simply mapping nucleotides to pixels resulted in noise, so I applied averaging over bases to obtain visually identifiable blocks of a certain colour intensity. By taking the average number of G's and C's in blocks of approximately 20-50 bases and mapping it to the 0-255 green intensity, I generated a structure of the genome that distinguished areas exhibiting distinct GC content structure, similar to how origins of replication occur in areas with higher A's and T's, where the DNA helix is more easily opened up by a helicase for DNA replication to begin.

The Visual Genome Browser is the culmination of more than 7 years of experimentation and it is now available in a Beta for people to start exploring genomes for themselves in this 2 Dimensional format.

Initially it will not be fully clear how this way to visualize the genome would be of benefit, but as I release more videos on the use cases it will become evident.