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Overview
We present a fast and accurate algorithm, NetCoffee, which allows to find a global alignment of multiple PPI networks. NetCoffee searches for a global alignment by maximizing a target function using simulated annealing (SA) on a set of weighted bipartite graphs that are constructed using a triplet approach similar to T-Coffee.
The main algorithm can be subsumed in the following four steps:
building the PPI networks and a library of bipartite graphs;
assigning an integrated weight to each edge in the bipartite graphs using a triplet extension approach similar to T-Coffee;
building a search space that consists of candidate edges (protein pairs);
simulated annealing (SA) with a large number of iterations of a Metropolis Scheme to maximize a scoring function for global alignments.
To assess its performance, NetCoffee was applied to four real
