Bioinformatics Vol. 18 no. 2 2002
Pages 351-361
© 2002 Oxford University Press
Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae
1 Max Delbrück
Center for Molecular Medicine, Department of Bioinformatics,
D-13092 Berlin-Buch, Germany
2 Ecology and Evolution, ETH Zentrum,
CH-8092 Zurich, Switzerland
3 Max Planck Institute for Molecular
Genetics, Department of Bioinformatics, D-14195 Berlin-Dahlem,
Germany
4 Biocomputing & Structures Program,
EMBL, D-69012 Heidelberg, Germany
5 University of Freiburg, Institute of
Molecular Medicine, D-79106 Freiburg, Germany
Received on March 2, 2001
; revised on September 14, 2001
; accepted on September 14, 2001
Motivation: Reconstructing and analyzing the metabolic map of microorganisms is an important challenge in bioinformatics. Pathway analysis of large metabolic networks meets with the problem of combinatorial explosion of pathways. Therefore, appropriate algorithms for an automated decomposition of these networks into smaller subsystems are needed.
Results: A decomposition algorithm for metabolic networks based on the local connectivity of metabolites is presented. Interrelations of this algorithm with alternative methods proposed in the literature and the theory of small world networks are discussed. The applicability of our method is illustrated by an analysis of the metabolism of Mycoplasma pneumoniae , which is an organism of considerable medical interest. The decomposition gives rise to 19 subnetworks. Three of these are here discussed in biochemical terms: arginine degradation, the tetrahydrofolate system, and nucleotide metabolism. The interrelations of pathway analysis of biochemical networks with Petri net theory are outlined.
Availability: METATOOLis available from ftp://mudshark.brookes.ac.uk/pub/software/ibmpc or http://www.bioinf.mdc-berlin.de/metabolic/. The program SEPARATORfor decomposing metabolic networks is available from http://www.bioinf.mdc-berlin.de/metabolic/.
Supplementary information: http://www.bioinf.mdc-berlin.de/metabolic/metatool/ http://www.bork.embl-heidelberg.de/Annot/MP/ (re-annotation of M. pneumoniae genome)
Contact: dandekar{at}embl-heidelberg.de; koch_i{at}molgen.mpg.de; pfeiffer{at}eco.umnw.ethz.ch; stschust{at}mdc-berlin.de
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