GraMoFoNe: a Cytoscape plugin for querying motifs without topology in Protein-Protein Interactions networks

Guillaume Blin (1) , Florian Sikora (1) , Stéphane Vialette (1)

1 LIGM - Laboratoire d'Informatique Gaspard-Monge

During the last decade, data on Protein-Protein Interactions (PPI) has increased in a huge manner. Searching for motifs in PPI Network has thus became a crucial problem to interpret this data. A large part of the literature is devoted to the query of motifs with a given topology. However, the biological data are, by now, so noisy (missing and erroneous information) that the topology of a motif can be unrelevant. Consequently, Lacroix et al. (TCBB 2006) defined a new problem, called GRAPH MOTIF, which consists in searching a multiset of colors in a vertex-colored graph. In this article, we present GraMoFoNe, a plugin to Cytoscape based on a Linear Pseudo-Boolean optimization solver which handles GRAPH MOTIF and some of its extensions.

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]; Algorithme et structure de données [cs.DS]

Guillaume Blin, Florian Sikora, Stéphane Vialette. GraMoFoNe: a Cytoscape plugin for querying motifs without topology in Protein-Protein Interactions networks. Bioinformatics and Computational Biology (BICoB'10), Mar 2010, Honolulu, United States. pp.38-43. ⟨hal-00425661⟩