Abstract: Agenetic algorithm(GA) using integer coding and node based crossover method, and its application in studying The chemical subgraph isomorphism were described in this paper.Aninitial population of random chromosomes representing the mapping betweent arget structure and query structure nodes is evolved by The GA to better solutions until anoptimal solution, the correct mapping, is found.Both The chemical subgraph isomorphism and The multi subgraph isomorphism were implemented.

Key words: Genetic algorithms, Subg raph isomorphism, Substructure searching