Protein-protein Interaction Network Alignment: Algorithms and Tools

This chapter reviews the state of the art and analyzes and compares various aspects of available protein-protein interaction (PPI) network alignment algorithms. In particular, the following facets are considered: (1) adopted network model, (2) similarity measures exploited to assess protein similarity, (3) local versus global PPI network alignment, (4) pairwise versus multiple PPI network alignment, (5) additional biological information exploited (e.g., phylogenetic information), (6) validation method, and (7) data used for the evaluation. The remainder of the chapter provides some background information along with a basic comparison of the PPI network alignment techniques, focusing on points 1-4. A section briefly describes the algorithms and tools and compares them on point (5). Another section carries out a coarse-grain comparison with respect to points (6) and (7). Finally, the chapter discusses the strengths and weaknesses of the approaches considered and draws some conclusions.