We describe algorithms for pattern matching and pattern
learning in TOPS diagrams (formal descriptions of protein topologies).
These problems can be reduced to checking for subgraph isomorphism
and finding maximal common subgraphs in a restricted class of ordered
graphs. We have developed a subgraph isomorphism algorithm for
ordered graphs, which performs well on the given set of data. The
maximal common subgraph problem then is solved by repeated
subgraph extension and checking for isomorphisms. Despite the
apparent inefficiency such approach gives an algorithm with time
complexity proportional to the number of graphs in the input set and is
still practical on the given set of data. As a result we obtain fast
methods which can be used for building a database of protein
topological motifs, and for the comparison of a given protein of known
secondary structure against a motif database