Metabolic network visualization eliminating node redundance and preserving metabolic pathways |
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Authors: | Romain Bourqui Ludovic Cottret Vincent Lacroix David Auber Patrick Mary Marie-France Sagot Fabien Jourdan |
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Institution: | 1. LaBRI, Université Bordeaux I, 351 Cours de la libération, 33405, Talence CEDEX, France 2. BAOBAB Team, Inria Rh?ne-Alpes, Projet HELIX, Université de Lyon ; université Lyon 1 ; CNRS ; UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 43 boulevard du 11 novembre 1918, Villeurbanne, F-69622, France 3. UMR1089 Xénobiotiques INRA-ENVT, ?, 180 chemin de Tournefeuille – St-Martin-du-Touch, BP 3, 31931, Toulouse CEDEX, France
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Abstract: | Background The tools that are available to draw and to manipulate the representations of metabolism are usually restricted to metabolic
pathways. This limitation becomes problematic when studying processes that span several pathways. The various attempts that
have been made to draw genome-scale metabolic networks are confronted with two shortcomings: 1- they do not use contextual
information which leads to dense, hard to interpret drawings, 2- they impose to fit to very constrained standards, which implies,
in particular, duplicating nodes making topological analysis considerably more difficult. |
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