CytoMCL: A Cytoscape plugin for fast clustering of protein interaction networks

The analysis of the whole set of molecular interactions in an organism, often referred to as interaction networks, is becoming an important research area. A main approach for such analysis resides on the application of clustering techniques to such networks. The meaning of discovered clusters, (i.e. highly interconnected regions), is strictly related to the type of networks. For instance in protein-protein interaction networks clusters may represent protein complexes. The Markov Clustering Algorithm (MCL) is a wellknown algorithm for clustering graphs. It does not provide a graphical user interface and cannot be used in the Cytoscape platform. We present CytoMCL a Cytoscape plugin that finds clusters in a graph by using MCL. It is based on an intuitive interface it is able to load a network from Cytoscape, to analyze it and to visualize resulting clusters into Cytoscape.