GraMoFoNe

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 21/04/10
  • Minor correction: 21/04/10
Keywords

GraMoFoNe : a Plugin for Cytoscape

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System: UNIX-like, Windows, MacOS X
  • Current version: 0.1 - 30/03/2010
  • License(s): GPL
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): Florian Sikora
  • Contact designer(s): sikora @ univ-mlv.fr
  • Laboratory, service: LIGM

 

General software features

GraMoFoNe (Graph Motif For Networks) is developed as a plugin for Cytoscape Fiche Plume. Cytoscape is an open-source software platform for network visualization and analysis, which supports the development of external plugin tools to extend its functionalities.

Our plugin seeks for connected occurrences of a motif (set or multiset of proteins), given by the user, into a Protein-Protein Interaction network previously loaded into the Cytoscape workspace (many file formats are supported). Similarity is measured among sequence-similarity via a Blastp analysis: proteins in the motif got different colors, proteins of the network are colored with the colors of motif proteins which are homologous.

Note that a network node can have 0, 1 or more colors. GraMoFoNe allows deletions (proteins in the motif but not in the resulting connected subnetwork), and insertions (proteins in the results but not in the motif)
of colored or uncolored network nodes.

Context in which the software is used

It is an implementation of a known algorithmic problem in a widely used platform.

Publications related to the software

Guillaume Blin, Florian Sikora, and Stéphane Vialette. GraMoFoNe: a Cytoscape plugin for querying motifs without topology in Protein-Protein Interactions networks. In, Hisham Al-Mubaid, editors, 2nd International Conference on Bioinformatics and Computational Biology (BICoB'10). Honolulu, USA. 24-26 March 2010. pp. 38?43.International Society for Computers and their Applications (ISCA). Note: hal-00425661