Computing graphlet signatures of network nodes and motifs in Cytoscape with GraphletCounter | Zendy

Christopher W. Whelan | Zendy; Kemal Sönmez | Zendy

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Computing graphlet signatures of network nodes and motifs in Cytoscape with GraphletCounter

Author(s) -

Christopher W. Whelan,

Kemal Sönmez

Publication year - 2011

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btr637

Subject(s) - workflow , plug in , computer science , software , java , biological network , network analysis , data mining , software tool , visualization , operating system , bioinformatics , database , physics , quantum mechanics , biology

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.

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