NABEECO: Biological network alignment with bee colony optimization algorithm

Motivation: A growing number of biological networks of ever increasing sizes are becoming available nowadays, making the ability to solve Network Alignment of primer importance. However, computationally the problem is hard for data sets of real-world sizes. Results: we developed NABEECO, a novel and robust Network Alignment heuristic based on Bee Colony Optimization. We use the so-called Graph Edit Distance (GED) as optimization criterion, which is defined as the minimal amount of edge and node modifications necessary to transform one graph into another. We compare NABEECO on a set of protein-protein interaction networks to the current state of the art tool for biological networks, MI-GRAAL. Conclusion: We present the first Bee Colony Optimization algorithm for biological Network Alignment. NABEECO, in contrast to many other tools, can be applied to all kinds of networks and allows incorporating prior knowledge about node/edge similarity, though this is not required a priori. NABEECO together with a more detailed description and all data sets used are publicly available at http://nabeeco.mpi- inf.mpg.de.