What is GraMoFoNe
GraMoFoNe (Graph Motif For Networks) is under GPL licence, written in Java 1.6 and developed as a plugin for Cytoscape. Cytoscape is an open-source software platform for network visualization and analysis, which supports the development of external plugin tools extending its functionality.
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 format 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.
It uses an exact algorithm to perform this task. To this end, we choose to express our problem as a linear pseudo-boolean optimization problem (LPB), i.e. as a linear program whose variables are boolean. We choose Sat4JPseudo.
- Cytoscape (has to be installed to run the plugin)
- Blast (has to be installed to run the plugin)
- GraMoFoNe Version 0.1 (2009-10)
- The easiest way to install GraMoFoNe is to use the "Manage Plugin" menu in Cytoscape software
- Plugin Jar. Recommended. Save this file in the Cytoscape's Plugin directory.
- Source Code. If you want to modify GraMoFoNe. (The plugin (sources, javadoc, external libraries) and dirty program for batch tests)
- PPI Networks (from Torque website) as .sif files (can be imported in Cytoscape). Date : 2009-08.
- Motifs (kindly supplied by Torque authors) as .txt files. One motif by line, tab separated, with the name of the motif as the first tab. Date : 2009-08.
- Fasta Files (from Torque website for the Yeast, Human and Fly, from Biomart for Bovine, Mouse and Yeast, all six manually completed from Uniprot). Contains sequence information for proteins in the Fasta format (>id on the first line, then the sequence). Date : 2009-08.
Help and Snapshots
If you use GraMoFoNe, please cite the following :
- 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
For any questions, remarks, suggestions, advices, bugs, please contact Florian Sikora
sikora (at) univ-mlv (dot) fr