A software tool and Cytoscape plugin for computing graphlet degree signatures of nodes and motifs in biological networks
GraphletCounter is an open-source software tool for computing the graphlet signatures of nodes and motifs in biological networks. GraphletCounter can operate on its own or as a plugin to the network analysis environment Cytoscape. GraphletCounter computes the graphlet signatures of individual nodes or of motifs, which can be specified by files generated by the motif-finding tool mfinder. It displays graphlet signatures visually within Cytoscape, and can output graphlet data for integration with larger workflows. Graphlet signatures were introduced by the Przulj group at the University of California at Irvine; please see the following references:
Przulj, N. (2007) Biological network comparison using graphlet degree distribution. Bioinformatics, 23(2), e177-e183.
Milenkovic, T. and Przulj, N. (2008) Uncovering Biological Network Function via Graphlet Degree Signatures. Cancer Informatics, 6, 257-273.
Also refer to the mfinder home page for information on motif finding and a description of its output file format.
View the README file for GraphletCounter.
UPDATE: GraphletCounter now has a project website at Google code. Go there to check out the source code, and add your own improvements.
To install GraphletCounter into Cytoscape, chose “Manage Plugins” from the Plugins menu and enter http://www.csee.ogi.edu/~whelanch/graphletcounter/plugin_descriptor.xml as a new download site.
Or, download the source and binaries, and copy the file plugin/GraphletCounter.jar into the plugins directory of your Cytoscape installation: GraphletCounter-1.2.tgz
GraphletCounter is free, open source software distributed under the LGPL. Please let us know if you find it helpful or modify it!
Whelan, C., & Sonmez, K. (2012). Computing graphlet signatures of network nodes and motifs in Cytoscape with GraphletCounter. Bioinformatics, 28(2), 290–291. doi:10.1093/bioinformatics/btr637