NetMatchStar: an enhanced Cytoscape network querying app [version 1; referees: 2 approved]

Authors :: Fabio Rinnone
Giovanni Micale
Vincenzo Bonnici
Gary D. Bader
Dennis Shasha
Alfredo Ferro
Alfredo Pulvirenti
Rosalba Giugno
Author Affiliations :: <relatesTo>1</relatesTo>Department of Maths and Computer Science, University of Catania, Catania, 95125, Italy<br /><relatesTo>2</relatesTo>Department of Computer Science, University of Verona, Verona, 37134, Italy<br /><relatesTo>3</relatesTo>The Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada<br /><relatesTo>4</relatesTo>Department of Computer Science,, Courant Institute of Mathematical Sciences, New York University, New York, NY, 10012, USA<br /><relatesTo>5</relatesTo>Department of Clinical and Experimental Medicine, University of Catania, Catania, 95125, Italy
Source :: F1000Research. 4:479
Publication Year :: 2015
Publisher :: London, UK: F1000 Research Limited, 2015.
Abstract: We present NetMatchStar, a Cytoscape app to find all the occurrences of a query graph in a network and check for its significance as a motif with respect to seven different random models. The query can be uploaded or built from scratch using Cytoscape facilities. The app significantly enhances the previous NetMatch in style, performance and functionality. Notably NetMatchStar allows queries with wildcards.

Subjects :: Software Tool Article
Articles
Bioinformatics
Theory & Simulation
network querying
exact graph matching
approximate graph matching
cytoscape app
statistical significance
background network models
randomization
biological network motifs

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