The purpose of this thesis is to perform an analysis of approaches to querying chemical databases and to validate or invalidate its results. Currently, there exists no work which would compare the performance and memory usage of the best performing approaches on the same data set. In this thesis, we address this lack of information and we create an un-biased benchmark of the most popular index building methods for subgraph querying of chemical databases. Also, we compare the results of such benchmark with the performance results of an SQL and a graph database. 1

This project introduces history and basic notions of the graph theory. It describes graph theory problems, possible graph representations and practical graph management in databases. Aims to subgraph and graph isomorphism. It describes possible ways to find graph isomorphism and chosen algorithms for subgraph and graph isomorphism. The experimental part aims to comparing two implemented algorithms. These are Ullmann and VF2 algorithm. Also searches difference between graphs stored in memory and graphs stored in database.