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

Abstract : 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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Submitted on : Thursday, October 22, 2009 - 5:05:01 PM
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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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