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Bioinformatics Vol. 19 Suppl. 2 2003
pages ii26-ii34
© 2003 Oxford University Press

Ab initio reconstruction of metabolic pathways

Frédéric Boyer 1,2 and Alain Viari 2,*

1 LSR-IMAG, 681, rue de la Passerelle, BP. 72, 38402 Saint Martin d’Hères Cedex, France
2 INRIA Rhône-Alpes, 655, avenue de l’Europe, Montbonnot, 38334 Saint Ismier Cedex, France

Received on March 17, 2003 ; accepted on June 9, 2003

We propose a new formulation for the problem of ab initio metabolic pathway reconstruction. Given a set of biochemical reactions together with their substrates and products, we consider the reactions as transfers of atoms between the chemical compounds and we look for successions of reactions transferring a maximal (or preset) number of atoms between a given source and sink compound. We state this problem as the one of finding a composition of partial injections that maximizes the image size. First, we study the theoretical complexity of this problem, state some related problems and then give a practical algorithm to solve them. Finally, we present two applications of this approach to the reconstruction of the tryptophan biosynthesis pathway and to the glycolysis.

Contact: alain.viari{at}inrialpes.fr

* To whom correspondence should be addressed.


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