“Master-Slave ” Biological Network Alignment

Abstract. Performing global alignment between protein-protein interaction (PPI) networks of different organisms is important to infer knowledge about conserva-tion across species. Known methods that perform this task operate symmetrically, that is to say, they do not assign a distinct role to the input PPI networks. How-ever, in most cases, the input networks are indeed distinguishable on the basis of how well the corresponding organism is biologically well-characterized. For well-characterized organisms the associated PPI network supposedly encode in a sound manner all the information about their proteins and associated interac-tions, which is far from being the case for not well characterized ones. Here the new idea is developed to devise a method for global alignment of PPI networks that in fact exploit differences in the characterization of organisms at hand. We assume that the PPI network (called Master) of the best characterized is used as a fingerprint to guide the alignment process to the second input network (called Slave), so that generated results preferably retain the structural characteristics of the Master (and using the Slave) network. We tested our method showing that the results it returns are biologically relevant.