title: Computing graphlet signatures of network nodes and motifs in Cytoscape with GraphletCounter.
abstract: Biological network analysis can be enhanced by examining the connections between nodes and the rest of the network. For this purpose we have developed GraphletCounter, an open-source software tool for computing graphlet degree signatures that can operate on its own or as a plug-in to the network analysis environment Cytoscape. A unique characteristic of GraphletCounter is its ability to compute the graphlet signatures of network motifs, which can be specified by files generated by the motif-finding tool mfinder. GraphletCounter displays graphlet signatures for visual inspection within Cytoscape, and can output graphlet data for integration with larger workflows.
  
  
  METHODS
  GraphletCounter is implemented in Java. It can be downloaded from the Cytoscape plugin repository, and is also available at http://sonmezsysbio.org/software/ graphletcounter.
authors.affiliation: Biomedical Engineering, Oregon Health and Science University, 20000 NW Walker Road, Beaverton, OR 97006, USA. whelanch@ohsu.edu
authors.forename: Christopher
authors.initials: C
authors.lastname: Whelan
authors.forename: Kemal
authors.initials: K
authors.lastname: Sönmez
mesh_terms: D006801:Humans; D012984:Software; D049490:Systems Biology / Q000379:methods*; D014584:User-Computer Interface