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Comparing Metabolic Pathways through Reactions and Potential Fluxes

  • Paolo Baldan
  • Nicoletta Cocco
  • Federica Giummolè
  • Marta Simeoni
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8100)

Abstract

Comparison of metabolic pathways is useful in phylogenetic analysis and for understanding metabolic functions when studying diseases and in drugs engineering. In the literature many techniques have been proposed to compare metabolic pathways. Most of them focus on structural aspects, while behavioural or functional aspects are generally not considered. In this paper we propose a new method for comparing metabolic pathways of different organisms based on a similarity measure which considers both homology of reactions and functional aspects of the pathways. The latter are captured by relying on a Petri net representation of the pathways and comparing the corresponding T-invariant bases, which represent minimal subsets of reactions that can operate at a steady state. A prototype tool, CoMeta, implements this approach and allows us to test and validate our proposal. Some experiments with CoMeta are presented.

Keywords

Metabolic Pathway Metabolic Network Glycolysis Pathway Stoichiometric Matrix Full Network 
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 2013

Authors and Affiliations

  • Paolo Baldan
    • 1
  • Nicoletta Cocco
    • 2
  • Federica Giummolè
    • 2
  • Marta Simeoni
    • 2
  1. 1.Dipartimento di MatematicaUniversità di PadovaItaly
  2. 2.DAISUniversità Ca’ Foscari VeneziaItaly

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