The C3Part/Isofun package implements a generic approach to the local alignement of two or more graphs representing biological data, such as genomes, metabolic pathways or protein-protein interactions, in order to infer functional coupling between them. Complete description of the theory can be found in the following papers:

[1] Syntons, Metabolons and Interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data. F. Boyer, A. Morgat, L. Labarre, J. Pothier and A. Viari Bioinformatics 21:4209-4215 (2005)
[2] Multiple alignment of biological networks: A flexible approach. Y.-P. Deniélou, F. Boyer, M.-F. Sagot, and A. Viari. In CPM'09, volume 5542 of Lecture Notes in Computer Science, pages 173-185. Springer-Verlag, 2009.
[3] Bacterial syntenies an exact approach with quorum. Y.-P. Deniélou, F. Boyer, M.-F. Sagot, and A. Viari. BMC Bioinformatics - submitted 2011
The standard distribution contains :
  • Java source code
  • Optional Shell scripts to run the main program (under Unix)
  • samples data files
  • documentation
  • Java 1.6.0 (or 1.5.0)
C3P/Isofun is distributed under the LGPL Licence.

The distribution can be downloaded here : Isofun.zip

It will expand as a directory named "Isofun"
Please read the README file located at the distribution root
and the user's guide located in the "docs" directory.
For more information, please contact : Alain Viari