CFinder: locating cliques and overlapping modules in biological networks

Bioinformatics. 2006 Apr 15;22(8):1021-3. doi: 10.1093/bioinformatics/btl039. Epub 2006 Feb 10.


Most cellular tasks are performed not by individual proteins, but by groups of functionally associated proteins, often referred to as modules. In a protein association 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

Supplementary information: Supplementary data are available on Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biology / methods
  • Cell Physiological Phenomena
  • Computer Graphics*
  • Databases, Protein*
  • Information Storage and Retrieval / methods*
  • Proteins / metabolism*
  • Signal Transduction / physiology*
  • Software*
  • User-Computer Interface*


  • Proteins