Architecture frequencies

The frequency of an architecture is computed as the fraction of the representative proteins with exactly that architecture. The frequency of a domain A -> domain B connection is computed as the fraction of the representative proteins containing that pair of domains in that order. For clarity of visualization, architectures are filtered for sufficient frequency, and the domains and edges are presented as graphs drawn by the Graphviz software [82] via the python pygraphviz package [83], with a custom script setting graphical parameters and laying out domains on the page according to frequency of the position of the domain between N- and C-terminus.