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Bioinformatics Advance Access originally published online on February 3, 2007
Bioinformatics 2007 23(7):910-912; doi:10.1093/bioinformatics/btm032
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

NetMatch: a Cytoscape plugin for searching biological networks

A. Ferro 1,*, R. Giugno 1, G. Pigola 1, A. Pulvirenti 1, D. Skripin 1, G. D. Bader 2 and D. Shasha 3

1Dipartimento di Matematica e Informatica, Università di Catania, Viale A. Doria 6, I-95125 Catania, Italy, 2Banting and Best Department of Medical Research and Department of Medical Genetics and Microbiology, University of Toronto, 160 College St, Toronto, Ontario, Canada M5S 3E1 and 3Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street New York, NY 10012, USA

*To whom correspondence should be addressed.


  Abstract

Summary: NetMatch is a Cytoscape plugin which allows searching biological networks for subcomponents matching a given query. Queries may be approximate in the sense that certain parts of the subgraph-query may be left unspecified. To make the query creation process easy, a drawing tool is provided. Cytoscape is a bioinformatics software platform for the visualization and analysis of biological networks.

Availability: The full package, a tutorial and associated examples are available at the following web sites: http://alpha.dmi.unict.it/~ctnyu/netmatch.html, http://baderlab.org/Software/NetMatch

Contact: ferro{at}dmi.unict.it

Associate Editor: Chris Stoeckert

Received on October 31, 2006; revised on January 24, 2007; accepted on January 24, 2007

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