Bioinformatics Advance Access originally published online on February 10, 2006
Bioinformatics 2006 22(8):1021-1023; doi:10.1093/bioinformatics/btl039
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CFinder: locating cliques and overlapping modules in biological networks
1 Department of Biological Physics, Eötvös University Pázmány P. stny. 1A, H-1117 Budapest, Hungary
2 Biological Physics Research Group of the Hungarian Academy of Sciences Pázmány P. stny. 1A, H-1117 Budapest, Hungary
*To whom correspondence should be addressed.
Summary: Most cellular tasks are performed not by individual proteins, but by groups of functionally associated proteins, often referred to as modules. In a protein assocation network modules appear as groups of densely interconnected nodes, also called communities or clusters. These modules often overlap with each other and form a network of their own, in which nodes (links) represent the modules (overlaps). We introduce CFinder, a fast program locating and visualizing overlapping, densely interconnected groups of nodes in undirected graphs, and allowing the user to easily navigate between the original graph and the web of these groups. We show that in gene (protein) association networks CFinder can be used to predict the function(s) of a single protein and to discover novel modules. CFinder is also very efficient for locating the cliques of large sparse graphs.
Availability: CFinder (for Windows, Linux and Macintosh) and its manual can be downloaded from http://angel.elte.hu/clustering.
Supplementary information: Supplementary data are available on Bioinformatics online.
Contact: cfinder{at}angel.elte.hu
Received on December 19, 2005; revised on February 1, 2006; accepted on February 2, 2006
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