Querying Graphs in Protein-Protein Interactions Networks Using Feedback Vertex Set

Recent techniques increase rapidly the amount of our knowledge on interactions between proteins. The interpretation of these new information depends on our ability to retrieve known sub-structures in the data, the Protein-Protein Interactions (PPI) networks. In an algorithmic point of view, it is an hard task since it often leads to NP-hard problems. To overcome this difficulty, many authors have provided tools for querying patterns with a restricted topology, i.e. paths or trees in PPI networks. Such restriction leads to the development of fixed parameter tractable (FPT) algorithms, which can be practicable for restricted sizes of queries. Unfortunately, GRAPH HOMOMORPHISM is a W[1]-hard problem, and hence, no FPT algorithm can be found when patterns are in the shape of general graphs. However, Dost et al. [2] gave an algorithm (which is not implemented) to query graphs with a bounded treewidth in PPI networks (the treewidth of the query being involved in the time complexity). In thi...

• Type: Journal
• Year: 2010
• Where: TCBB
• Authors: Guillaume Blin, Florian Sikora, Stéphane Vialette
• Keywords: Algorithm, Feedback Vertex, Ppi Network, Software Engineering, TCBB 2010