GraMoFoNe: a Cytoscape plugin for querying motifs without topology in Protein-Protein Interactions networks - Archive ouverte HAL
Communication Dans Un Congrès Année : 2010

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

Résumé

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.
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Dates et versions

hal-00425661 , version 1 (22-10-2009)

Identifiants

  • HAL Id : hal-00425661 , version 1

Citer

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⟩
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