. B. Fig, Les deux sous-structures entre une molécule de pyruvate et une molécule de sérine correspondant aux solutions du problème Sous-graphe Induit Commun (Connexe) Maximal -(a) montre la plus grande sous-structure commune, de taille 5, entre les deux graphe moléculaires et (b) la clique associée dans le graphe de correspondance , (c) montre la plus grande sous-structure connexe commune qui est elle de taille 4 et (d) la clique associée dans le graphe de correspondance B.2. Résolution du problème Sous-graphe Induit Commun Maximal avec le graphe de correspond Procédure Branch-and-Bound Paramètre : Entier : meilleurTaille, Ensemble-d-ensembles-de-noeuds : meilleursSolutions, Ensemble-de-noeuds : solutionCourante, Ensemble-de-noeuds : noeudsCompatibles

?. and ?. {solutioncourante}, On continue l'exploration en profondeur */ pour chaque s ? noeudsCompatibles faire noeudsCompatibles ? noeudsCompatibles \ {s}; nouveaux ? noeuds de noeudsCompatibles reliés à s; si (|solutionCourante| + |nouveaux| + 1) ? meilleurTaille alors Branch-and-Bound(meilleurTaille, meilleursSolutions, solutionCourante ? {s}, nouveaux)

. B. Fig, Identification de stables dans le graphe de correspondance lors de sa construction -Les noeuds du graphe de correspondance qui sont réunis au sein d'un même groupe proposent tous une correspondance pour un même noeud d'un des deux graphes initiaux et ne peuvent donc pas faire partie de la même solution B.2. Résolution du problème Sous-graphe Induit Commun Maximal avec le graphe de correspond Procédure B-a-B-Corres Paramètre : Entier : meilleurTaille, Ensemble-d-ensemble-de-noeuds : meilleursSolutions, Ensemble-de-noeuds : solutionCourante, Ensemble-d-ensemble-de-noeuds : noeudsCompatibles

?. and ?. {solutioncourante}, On continue l'exploration en profondeur */ pour chaque groupeDeNoeuds ? noeudsCompatibles faire pour chaque s ? groupeDeNoeuds faire groupeDeNoeuds ? groupeDeNoeuds \ {s}; pour chaque groupeCourant ? noeudsCompatibles faire groupeCourant ? noeuds de groupeCourant reliés à s; si groupeCourant = ? alors nouveaux ? nouveaux ? groupeCourant

. Fin-programme-paramètre, Ensemble-d-ensemble-de-noeuds : g

. Si-le-problème-de-décision-associé-est, complet' pour sa classe de complexité, on dit que le problème d'optimisation est 'difficile'pour cette classe de complexité Exemple : le problème d'optimisation Clique Maximale qui consiste à trouver une Bibliographie ] Tatsuya Akutsu. Efficient extraction of mapping rules of atoms from enzymatic reaction data, Proceedings of the International Conference on Research in Computational Biology, pp.1-8, 2003.

B. Albert, Statistical mechanics of complex networks, Reviews of Modern Physics, vol.74, issue.1, pp.47-97, 2002.
DOI : 10.1103/RevModPhys.74.47

. Altshull, Gapped blast and psiblast : a new generation of protein database searche programs, Nucleic acids research, issue.17, pp.253389-3402, 1997.

]. Arita, Graph modeling of metabolism, Journal of Japanese Society for Artificial Intelligence, vol.15, pp.703-710, 2000.

]. Arita, Metabolic reconstruction using shortest paths. Simulation Practice and Theory, pp.109-125, 2000.

]. Bairoch, The ENZYME database in 2000, Nucleic Acids Research, vol.28, issue.1, pp.304-305, 2000.
DOI : 10.1093/nar/28.1.304

K. Arvind and . Bansal, A framework of automated reconstruction of microbial metabolic pathways, Proceedings of the IEEE International Symposium on Bioinformatics and Biomedical Engineering, 2000.

K. Arvind and . Bansal, Integrating co-regulated gene-groups and pair-wise genome comparisons to automate reconstruction of microbial pathways, Proceedings of the IEEE International Symposium on Bio-informatics and Biomedical Engineering, 2001.

. Barabási, Mean-field theory for scale-free random networks, Physica A: Statistical Mechanics and its Applications, vol.272, issue.1-2, pp.173-187, 1999.
DOI : 10.1016/S0378-4371(99)00291-5

A. Barrat and M. Weigt, On the properties of smallworld network models, Eur. Phys. J. B, 2000.

. Bateman, The Pfam Protein Families Database, Nucleic Acids Research, vol.30, issue.1, pp.276-280, 2002.
DOI : 10.1093/nar/30.1.276

URL : https://hal.archives-ouvertes.fr/hal-01294685

. Birget, PSPACE-complete problems for subgroups of free groups and inverse finite automata, Theoretical Computer Science, vol.242, issue.1-2, pp.247-281, 2000.
DOI : 10.1016/S0304-3975(98)00225-4

. Bize, Classification de séquences protéiques : modélisation d'un critère de similitude en utilisant une typologie sur les relations entre protéines, Proceedings of the Journées ouvertes de Biologie, Informatique et Mathématiques, pp.143-150, 2001.

. Blumenthal, A global analysis of Caenorhabditis elegans operons, Nature, vol.98, issue.6891, pp.851-853, 2002.
DOI : 10.1038/nature00831

. Bono, Reconstruction of Amino Acid Biosynthesis Pathways from the Complete Genome???Sequence, Genome Research, vol.8, issue.3, pp.203-210, 1998.
DOI : 10.1101/gr.8.3.203

. Brazma, Approaches to the Automatic Discovery of Patterns in Biosequences, Journal of Computational Biology, vol.5, issue.2, pp.279-305, 1998.
DOI : 10.1089/cmb.1998.5.279

K. Bron, J. Bron, and . Kerbosch, Algorithm 457: finding all cliques of an undirected graph, Communications of the ACM, vol.16, issue.9, pp.575-577, 1973.
DOI : 10.1145/362342.362367

L. Bruce and . Clarke, Stoichiometric network analysis, Cell biophysics, 1988.

J. Stuart and . Cordwell, Microbial genomes and " missing " enzymes : redefining biochemical pathways, Archives of Microbiology, vol.172, pp.269-279, 1999.

. Corpet, ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons, Nucleic Acids Research, vol.28, issue.1, pp.267-269, 2000.
DOI : 10.1093/nar/28.1.267

URL : https://hal.archives-ouvertes.fr/hal-00427044

K. Crescenzi, . Crescenzi, . Vigo-kann, and . Dandekar, A compendium of np optimization problems Pathway alignment : application to the comparative analysis of glicolytic enzymes, Biochem. J, vol.343, pp.115-124, 1998.

. Durbin, Biological sequence analysis : probabilistic models of proteins and nucleic acids, 1998.
DOI : 10.1017/CBO9780511790492

R. Sean and . Eddy, Profile hidden markov models, Bioinformatics, vol.14, issue.9, pp.755-763, 1998.

. Ellis, The University of Minnesota Biocatalysis/Biodegradation Database: emphasizing enzymes, Nucleic Acids Research, vol.29, issue.1, pp.340-343, 2001.
DOI : 10.1093/nar/29.1.340

. Ermolaeva, Prediction of operons in microbial genomes, Nucleic Acids Research, vol.29, issue.5, pp.1216-1221, 2000.
DOI : 10.1093/nar/29.5.1216

. Falquet, The PROSITE database, its status in 2002, Nucleic Acids Research, vol.30, issue.1, pp.235-238, 2002.
DOI : 10.1093/nar/30.1.235

. Fan, A graph-theoretic method to identify candidate mechanisms for deriving the rate law of a catalytic reaction, Computers & Chemistry, vol.26, issue.3, pp.265-292, 2002.
DOI : 10.1016/S0097-8485(01)00119-X

A. David, A. Fell, and . Wagner, BioThermoKinetics 2000 - Animating the cellular map, chapter 12 Structural properties of metabolic networks : implications for evolution and modelling of metabolism, 2000.

M. Walter and . Fitch, Distinguishing homologous from analogous proteins, Systematic zoology, vol.19, issue.2, pp.99-113, 1970.

M. Walter and . Fitch, Homology a personnal view on some of the problems, Trends in genetics, vol.16, issue.5, pp.227-231, 2000.

W. Robert and . Floyd, Algorithm 97 -shortest path, Communications of the ACM, vol.6, issue.5, p.345, 1962.

. Fujibuchi, Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping, Nucleic Acids Research, vol.28, issue.20, pp.4029-4036, 2000.
DOI : 10.1093/nar/28.20.4029

S. Gaasterland, E. Gaasterland, and . Selkov, Reconstruction of metabolic networks using incomplete information, Proceedings of the International Conference on Intelligent Systems for Molecular Biology, 1995.

. Gagneur, Hierarchical analysis of dependency in metabolic networks, Bioinformatics, vol.19, issue.8, pp.1027-1034, 2003.
DOI : 10.1093/bioinformatics/btg115

. Galperin, Analogous enzymes : independent inventions in enzyme evolution, Genome Research, vol.8, pp.779-790, 1998.

J. R. Garey, D. S. Garey, and . Johnson, Computers and intractability : a guide to the theory of NP-completeness, 1979.

. Gattiker, Alexandre Gattiker, 2003.

E. Auchincloss, T. Coudert, P. Lima, M. Kersey, C. J. Pagni et al., Automated annotation of microbial proteomes in swiss-prot, Computational Biology and Chemistry, vol.27, pp.49-58, 2003.

. Genrich, Executable petri net models for the analysis of metabolic pathways. Software Tools For Technology Transfer, DOI 10, 1007.

]. Goethals, Survey on frequent pattern mining, 2003.

. Goto, LIGAND: database of chemical compounds and reactions in biological pathways, Nucleic Acids Research, vol.30, issue.1, pp.402-404, 2002.
DOI : 10.1093/nar/30.1.402

. Gribskov, Profile scanning for three-dimensional structural patterns in protein sequences, Bioinformatics, vol.4, issue.1, pp.61-66, 1988.
DOI : 10.1093/bioinformatics/4.1.61

. Habib, Common connected components of interval graphs, 2003.
URL : https://hal.archives-ouvertes.fr/lirmm-00269548

. Haft, TIGRFAMs: a protein family resource for the functional identification of proteins, Nucleic Acids Research, vol.29, issue.1, pp.41-43, 2001.
DOI : 10.1093/nar/29.1.41

S. Happel, P. H. Happel, and . Sellers, THE CHARACTERIZATION OF COMPLEX SYSTEMS OF CHEMICAL REACTIONS, Chemical Engineering Communications, vol.16, issue.1, pp.221-240, 1989.
DOI : 10.1016/S0360-0564(08)60135-2

. Heiner, Analysis and simulation of steady states in metabolic pathways with petri nets, Proceedings of the Workshop on coloured Petri net, 2001.

. Huynen, Variation and evolution of the citric-acid cycle: a genomic perspective, Trends in Microbiology, vol.7, issue.7, pp.281-291, 1999.
DOI : 10.1016/S0966-842X(99)01539-5

. Huynen, Predicting Protein Function by Genomic Context: Quantitative Evaluation and Qualitative Inferences, Genome Research, vol.10, issue.8, pp.1204-1210, 2000.
DOI : 10.1101/gr.10.8.1204

. Itoh, Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes, Molecular Biology and Evolution, vol.16, issue.3, pp.332-346, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026114

J. , M. Jacob, and J. Monod, Genetic regulatory mechanisms in the synthesis of proteins, Journal of molecular biology, vol.3, pp.318-356, 1961.

. Jeong, The large-scale organisation of metabolic networks, Nature, vol.407, pp.651-653, 2000.

G. Kanehisa, S. Kanehisa, and . Goto, KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Research, vol.28, issue.1, pp.27-30, 2000.
DOI : 10.1093/nar/28.1.27

. Kanehisa, The kegg databases at genomenet. Nucleic acids research, pp.42-46, 2002.

R. Karp, D. Peter, M. Karp, and . Riley, Bioinformatics, database and systems, chapter 4 EcoCyc : The ressource and the lessons learned, 1999.

. Karp, Rapid identification of repeated patterns in strings, trees and arrays, Proceedings of the fourth annual ACM symposium on Theory of computing , STOC '72, pp.125-136, 1972.
DOI : 10.1145/800152.804905

. Karp, Integrated pathway???genome databases and their role in drug discovery, Trends in Biotechnology, vol.17, issue.7, p.17, 1999.
DOI : 10.1016/S0167-7799(99)01316-5

A. Paley and . Pellegrini-toole, The ecocyc and metacyc databases, Nucleic acids research, vol.28, issue.1, pp.56-59, 2000.

. Karp, The Pathway Tools software, Bioinformatics, vol.18, issue.Suppl 1, pp.225-232, 2002.
DOI : 10.1093/bioinformatics/18.suppl_1.S225

. Toole, The metacyc database Nucleic acids research, pp.59-61, 2002.

. Karp, The EcoCyc Database, Nucleic Acids Research, vol.30, issue.1, pp.56-58, 2002.
DOI : 10.1093/nar/30.1.56

M. Jon and . Kleinberg, Navigation in a small world, Science, vol.406, p.845, 2000.

]. Koch, Enumerating all connected maximal common subgraphs in two graphs, Theoretical Computer Science, vol.250, issue.1-2, pp.1-30, 2001.
DOI : 10.1016/S0304-3975(00)00286-3

. Dexter-kozen, Lower bounds for natural proof systems, Proceedings of the 18th IEEE Symposium on Foundations of Computer Science, pp.254-266, 1977.

. Küffner, Pathway analysis in metabolic databases via differential metabolic display (DMD), Bioinformatics, vol.16, issue.9, pp.825-836, 2000.
DOI : 10.1093/bioinformatics/16.9.825

. Lawrence, Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment, Science, vol.262, issue.5131, pp.208-213, 1993.
DOI : 10.1126/science.8211139

. Levi, A note on the derivation of maximal common subgraphs of two directed or undirected graphs, Calcolo, vol.3, issue.4, pp.341-351, 1972.
DOI : 10.1007/BF02575586

A. Ma, Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms, Bioinformatics, vol.19, issue.2, pp.270-277, 2003.
DOI : 10.1093/bioinformatics/19.2.270

. Marais, Metabolism and genetics of helicobacter pylori : the genome era. Microbiology and molecular biology reviews, pp.642-674, 1999.

. Matsuno, Hybrid petri net representation of gene regulatory network Special Issue : Petri Nets for Metabolic Networks, In Silico Biology, 2003.

. Mittenthal, Designing Metabolism: Alternative Connectivities for the Pentose Phosphate Pathway, Bulletin of Mathematical Biology, vol.60, issue.5, 1998.
DOI : 10.1006/bulm.1997.0043

. Mittenthal, A New Method for Assembling Metabolic Networks, with Application to the Krebs Citric Acid Cycle, Journal of Theoretical Biology, vol.208, issue.3, pp.361-382, 2001.
DOI : 10.1006/jtbi.2000.2225

W. Eugene and . Myers, Approximate matching of network expressions with spacers, Journal of Computational Biology, vol.3, issue.1, pp.33-51, 1996.

. Nakaya, Extraction of correlated gene clusters by multiple graph comparison, Genome Informatics, vol.12, pp.44-53, 2001.

. Nobeli, Irene Nobeli, Hannes Ponstingl, Eugene B. Krissinel, and Janet M, 2003.

. Thornton, A structure-based anatomy of the e. coli metabolome, Journal of Molecular Biology, vol.334, issue.4, pp.697-719, 2003.

. Ogata, A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters, Nucleic Acids Research, vol.28, issue.20, pp.4021-4028, 2000.
DOI : 10.1093/nar/28.20.4021

K. Ouzounis, C. A. Ouzounis, and P. D. Karp, Global Properties of the Metabolic Map of Escherichia coli, Genome Research, vol.10, issue.4, pp.568-576, 2000.
DOI : 10.1101/gr.10.4.568

. Overbeek, The use of gene clusters to infer functional coupling, Proceedings of the national academy of sciences of the USA, pp.2896-2901, 1999.
DOI : 10.1126/science.278.5338.631

. Overbeek, WIT2 : Metabolic reconstruction system, Bioinformatics, database and systems, 1999.

. Overbeek, WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction, Nucleic Acids Research, vol.28, issue.1, pp.123-125, 2000.
DOI : 10.1093/nar/28.1.123

K. Paley, M. Suzanne, P. D. Paley, and . Karp, Evaluation of computational metabolic-pathway predictions for Helicobacter pylori, Bioinformatics, vol.18, issue.5, pp.715-724, 2002.
DOI : 10.1093/bioinformatics/18.5.715

. Perrière, HOBACGEN: Database System for Comparative Genomics in Bacteria, Genome Research, vol.10, issue.3, pp.379-385, 2000.
DOI : 10.1101/gr.10.3.379

. Pfeiffer, METATOOL: for studying metabolic networks, Bioinformatics, vol.15, issue.3, pp.251-257, 1999.
DOI : 10.1093/bioinformatics/15.3.251

S. Pisanti, M. Pisanti, and . Sagot, Applied combinatorics on words, chapter Network expression inference, 2003.

. Podani, Comparable system-level organisation of archaea and eukaryotes, Nature Genetics, vol.29, issue.1, pp.54-56, 2001.
DOI : 10.1038/ng708

. Ravasz, Hierarchical Organization of Modularity in Metabolic Networks, Science, vol.297, issue.5586, pp.1551-1555, 2002.
DOI : 10.1126/science.1073374

. Liebman, Petri nets representations in metabolic pathways, Proceedings of the International Conference on Intelligent Systems for Molecular Biology, 1993.

. Reddy, Qualitative analysis of biochemical reaction systems, Computers in Biology and Medicine, vol.26, issue.1, pp.9-24, 1996.
DOI : 10.1016/0010-4825(95)00042-9

. Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in escherichia coli, Journal of molecular biology, vol.318, pp.911-932, 2002.

. Salgado, Operons in Escherichia coli: Genomic analyses and predictions, Proceedings of the national academy of sciences of the USA, pp.6652-6657, 2000.
DOI : 10.1016/S1359-0278(98)00069-8

. Salgado, RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12, César Bonavides-Martínez, and Julio Collado-Vides. Regulondb (versio 3.2) : transcriptional regulatiojn and operon organization in escherichia coli k12, pp.72-74, 2001.
DOI : 10.1093/nar/29.1.72

J. Walter and . Savitch, Relationship between nondeterministic and deterministic tape complexities, Journal of Computer and System Sciences, vol.4, pp.177-192, 1970.

. Schilling, Metabolic Pathway Analysis: Basic Concepts and Scientific Applications in the Post-genomic Era, Biotechnology Progress, vol.15, issue.3, pp.296-303, 1999.
DOI : 10.1021/bp990048k

. Schilling, Theory for the Systemic Definition of Metabolic Pathways and their use in Interpreting Metabolic Function from a Pathway-Oriented Perspective, Journal of Theoretical Biology, vol.203, issue.3, pp.229-248, 2000.
DOI : 10.1006/jtbi.2000.1073

. Schomburg, BRENDA: a resource for enzyme data and metabolic information, Trends in Biochemical Sciences, vol.27, issue.1, pp.54-56, 2002.
DOI : 10.1016/S0968-0004(01)02027-8

. Schuster, A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks, Nature Biotechnology, vol.18, issue.3, pp.326-332, 2000.
DOI : 10.1038/73786

. Schuster, Structural analysis of metabolic networks : elementary flux modes, analogy to petri nets, and application to mycoplasma pneumoniae, Proceedings of the German Conference on Bioinformatic, pp.115-120, 2000.

. Schuster, Reaction routes in biochemical reaction systems: Algebraic properties, validated calculation procedure and example from nucleotide metabolism, Journal of Mathematical Biology, vol.45, issue.2, pp.153-181, 2002.
DOI : 10.1007/s002850200143

. Selkov, A reconstruction of the metabolism of Methanococcus jannaschii from sequence data, Gene, vol.197, issue.1-2, 1997.
DOI : 10.1016/S0378-1119(97)00307-7

. Selkov, Functional analysis of gapped microbial genomes: Amino acid metabolism of Thiobacillus ferrooxidans, Proceedings of the national academy of sciences of the USA, pp.3509-3514, 2000.
DOI : 10.1126/science.282.5389.682

. Seo, Graph-theorical identification of pathways for biochemical reactions, Biotechnology Letters, vol.23, issue.19, pp.1551-1557, 2001.
DOI : 10.1023/A:1011913225764

B. Seressiotis, J. E. Seressiotis, and . Bailey, MPS: An artificially intelligent software system for the analysis and synthesis of metabolic pathways, Biotechnology and Bioengineering, vol.8, issue.6, pp.587-602, 1988.
DOI : 10.1002/bit.260310611

. Susumu, Organizing and computing metabolic pathway data in terms of binary relations Metabolism and evolution of haemophilus influenzae deduced from a whole-genome comparison with escherichia coli, Proceedings of the Pacific Symposium of Bioinformatics, pp.175-186279, 1996.

. Tatusov, A Genomic Perspective on Protein Families, Science, vol.278, issue.5338, pp.631-637, 1997.
DOI : 10.1126/science.278.5338.631

]. Valette, Les réseaux de petri, 2000.

. Van-helden, Bioinformatics and genome analysis, chapter Graph-based analysis of metabolic networks, pp.245-274, 2002.

A. Wagner and D. A. Fell, The small world inside large metabolic networks, Proceedings of the Royal Society B: Biological Sciences, vol.268, issue.1478, 2001.
DOI : 10.1098/rspb.2001.1711

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088812

]. Walsh, Search in small world, Proceedings of the International Joint Conference on Artificial Intelligence, 1999.

J. Duncan, S. H. Watts, and . Strogatz, Collective dynamics of 'small-world' networks, Nature, vol.393, pp.440-442, 1998.

D. Wittig, U. Beuckelaer, A. D. Wittig, and . Beuckelaer, Analysis and comparison of metabolic pathway databases, Briefings in Bioinformatics, vol.2, issue.2, pp.126-142, 2001.
DOI : 10.1093/bib/2.2.126

. Yada, Modeling and predicting transcriptional units of <$O_SSF>Escherichia coli<$C_SSF>genes using hidden Markov models, Bioinformatics, vol.15, issue.12, pp.15987-993, 1999.
DOI : 10.1093/bioinformatics/15.12.987

D. Yanai, C. Yanai, and . Delisi, The society of genes : networks of functional links between genes from comparative genomics, Genome Biology, vol.3, issue.11, 2002.
DOI : 10.4159/9780674495081

. Zheng, Computational Identification of Operons in Microbial Genomes, Genome Research, vol.12, issue.8, pp.1221-1230, 2002.
DOI : 10.1101/gr.200602