A review of aligners for protein protein interaction networks

Abstract

Protein Protein Interaction (PPI) can be considered as network. Alignment is the process of mapping nodes from one network to another network. The main objective of network alignment is to identify small, well defined interactome units such as protein complexes or conserved pathways that are analogous in the input network. Network alignment uncovers the relationship between protein complexes and functions. Similarity between two graph structures can be identified by evaluating the topology. Network alignment identifies either topological or sequential similarity. Gene annotations reveal the functional or sequential similarity and it can be evaluated based on semantic similarity. In this paper, we review the various network aligners and classify them according to the methodologies. We discuss the different evaluation metrics and the popular databases of protein interactions.