Pattern Matching in Protein-Protein Interaction Graphs

In the context of comparative analysis of protein-protein interaction graphs, we use a graph-based formalism to detect the preservation of a given protein complex (pattern graph) in the protein-protein interaction graph (target graph) of another species with respect to (w.r.t.) orthologous proteins. We give an efficient exponential-time randomized algorithm in case the occurrence of the pattern graph in the target graph is required to be exact. For approximate occurrences, we prove a tight inapproximability results and give four approximation algorithms that deal with bounded degree graphs, small ortholog numbers, linear forests and very simple yet hard instances, respectively. Email addresses: [email protected] (Gaëlle Brevier), [email protected] (Romeo Rizzi), [email protected] (Stéphane Vialette). Preprint submitted to Elsevier Science December 3, 2007