  The relationship between the design and functionality of molecular networks
is now a key issue in biology. Comparison of regulatory networks performing
similar tasks can give insights into how network architecture is constrained by
the functions it directs. We here discuss methods of network comparison based
on network architecture and signaling logic. Introducing local and global
signaling scores for the difference between two networks we quantify
similarities between evolutionary closely and distantly related bacteriophages.
Despite the large evolutionary separation between phage $\lambda$ and 186 their
networks are found to be similar when difference is measured in terms of global
signaling. We finally discuss how network alignment can be used to to pinpoint
protein similarities viewed from the network perspective.
