A blueprint shows you “what” but a genome doesn’t encode “what.” The genome can instead, be thought of as encoding a set of tools (proteins). It tells you nothing about what the function of each tool is, what the tools act on, how the tools act together or what the tools are used to build.

What makes genome analysis and visualization difficult is not only this deep interplay between its parts—how, when and why the tools are used—but also its physical architecture: the size and the density and distribution of functional regions. (Our genome is packed into 24 chromosomes, about 3 billion bases in all).

The first thing to note is that the tools (proteins) are not necessarily encoded by neighboring regions of the genome. For example, the code for four proteins that convert tyrosine to epinephrine are located on chromosomes 3, 9, 11 and 17. When we draw the chromosomes in their natural order and orientation this information is hidden.

Next, out of the 3 billion bases, not all have a well-defined job. Genes — which make up only about 33 percent of the genome — refer to segments of the genome that that code for proteins. But strictly speaking the term “coding regions” in the genome correspond only to specific staccato protein-coding sequences bundled within those larger genes. These segments are the exons (about 2.5 percent of the full genome, Figure 2). The rest of the genome (segments which are included both inside and outside gene regions) doesn’t have an obvious function—and has been disparagingly called “junk DNA”. However, junk DNA isn’t all junk and its role is hotly debated.