The detection of gene fusion events across genomes can be used for the 
prediction of functional associations of proteins, including physical 
interactions or complex formation. These predictions are obtained by the 
detection of similarity for pairs of 'component' proteins to 'composite' 
proteins. Since the amount of composite proteins is limited in nature, we 
augment this set by creating artificial fusion proteins from experimentally 
determined protein interacting pairs. The goal is to study the extent of protein 
interaction partners with increasing phylogenetic distance, using an automated 
method. We have thus detected component pairs within seven entire genome 
sequences of similar size, using artificially generated composite proteins that 
have been shown to interact experimentally. Our results indicate that protein 
interactions are not conserved over large phylogenetic distances. In addition, 
we provide a set of predictions for functionally associated proteins across 
seven species using experimental information and demonstrate the applicability 
of fusion analysis for the comparative genomics of protein interactions.