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Bioinformatics Advance Access originally published online on November 15, 2007
Bioinformatics 2008 24(2):282-284; doi:10.1093/bioinformatics/btm554
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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.

Computing topological parameters of biological networks

Yassen Assenov , Fidel Ramírez , Sven-Eric Schelhorn , Thomas Lengauer and Mario Albrecht *

Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany

*To whom correspondence should be addressed.


  Abstract

Summary: Rapidly increasing amounts of molecular interaction data are being produced by various experimental techniques and computational prediction methods. In order to gain insight into the organization and structure of the resultant large complex networks formed by the interacting molecules, we have developed the versatile Cytoscape plugin NetworkAnalyzer. It computes and displays a comprehensive set of topological parameters, which includes the number of nodes, edges, and connected components, the network diameter, radius, density, centralization, heterogeneity, and clustering coefficient, the characteristic path length, and the distributions of node degrees, neighborhood connectivities, average clustering coefficients, and shortest path lengths. NetworkAnalyzer can be applied to both directed and undirected networks and also contains extra functionality to construct the intersection or union of two networks. It is an interactive and highly customizable application that requires no expert knowledge in graph theory from the user.

Availability: NetworkAnalyzer can be downloaded via the Cytoscape web site: http://www.cytoscape.org

Contact: mario.albrecht{at}mpi-inf.mpg.de

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Martin Bishop

Received on June 16, 2007; revised on October 8, 2007; accepted on November 1, 2007

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