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Reaction Motifs in Metabolic Networks

  • Vincent Lacroix
  • Cristina G. Fernandes
  • Marie-France Sagot
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3692)

Abstract

The classic view of metabolism as a collection of metabolic pathways is being questioned with the currently available possibility of studying whole networks. Novel ways of decomposing the network into modules and motifs that could be considered as the building blocks of a network are being suggested. In this work, we introduce a new definition of motif in the context of metabolic networks. Unlike in previous works on (other) biochemical networks, this definition is not based only on topological features. We propose instead to use an alternative definition based on the functional nature of the components that form the motif. After introducing a formal framework motivated by biological considerations, we present complexity results on the problem of searching for all occurrences of a reaction motif in a network, and introduce an algorithm that is fast in practice in most situations. We then show an initial application to the study of pathway evolution.

Keywords

Bipartite Graph Metabolic Network Biochemical Network Subgraph Isomorphism Reaction Motif 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Vincent Lacroix
    • 1
    • 2
  • Cristina G. Fernandes
    • 3
  • Marie-France Sagot
    • 1
    • 2
    • 4
  1. 1.Équipe BAOBAB, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité Lyon IFrance
  2. 2.Projet HelixINRIA Rhône-AlpesFrance
  3. 3.Instituto de Matemática e EstatísticaUniversidade de São PauloBrazil
  4. 4.Department of Computer ScienceKing’s College LondonEngland

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