Abstract: This paper proposes a new methodology to disclose the functional information of complex metabolic network based on graph clustering algorithms and modular structure comparison, and indicates photosynthesis evolution in view of systems biology.In addition, two graph clustering algorithms, the Markov clustering and simulated annealing clustering, are introduced.The corresponding clustering results of chloroplast and cyanobacteria are presented.A similarity measure is defined to find the conservative functional module between chloroplast and cyanobacteria, and the overall structure of modules is compared with the counterparts in different species.

Key words: metabolic network, simulated annealing clustering, module similarity, Markov clustering