Figure 1.

Visualization of gene clusters sharing the same profiles (GPPP) in a two-dimensional space. Each circular node represents a gene cluster grouped by the same pair phylogenetic profile. The radius of the circle is proportional to the size of the cluster. The number shown at the center of each circle is the norm of the profile vector for this cluster. For a profile vector (x₁,x₂,x₃,...x_N), the norm of this profile is calculated by . All clusters are color-coded by COG's broad-function classification [25]. Links between clusters are present when the Hamming distance between two profiles is less than 5. We can see that for profiles with norms exceeding 10, similar profiles (Hamming distance less than 5), shown as clusters of connected nodes, tend to fall into the same functional category. When the profile norm is less than 10, broad functional categories for similar profiles begin to diverge. Several broad functions, for example, P (inorganic ion transport and metabolism), J (translation, ribosomal structure and biogenesis), and E (amino-acid transport and metabolism) can be well recognized by the phylogenetic method, while some are either absent or tend to mix with other broad functions. This shows the relative effectiveness of analyzing inheritance patterns of gene clusters for different broad functional categories. This figure is generated using the software package Pajek.s