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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Communication dans un congrès
Hisham Al-Mubaid. Bioinformatics and Computational Biology (BICoB'10), Mar 2010, Honolulu, United States. pp.38-43, 2010, International Society for Computers and their Applications (ISCA)


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Soumis le : jeudi 22 octobre 2009 - 17:05:01
Dernière modification le : mardi 28 octobre 2014 - 18:46:35
Document(s) archivé(s) le : mardi 16 octobre 2012 - 12:36:02

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  • HAL Id : hal-00425661, version 1

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Guillaume Blin, Florian Sikora, Stéphane Vialette. GraMoFoNe: a Cytoscape plugin for querying motifs without topology in Protein-Protein Interactions networks. Hisham Al-Mubaid. Bioinformatics and Computational Biology (BICoB'10), Mar 2010, Honolulu, United States. pp.38-43, 2010, International Society for Computers and their Applications (ISCA). <hal-00425661>

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