The ProDom MkDom2 API can be used to screen the ProDom database with the psi-blast program in order to cluster homologous domains. This API is routinely used to build each new release of ProDom. It relies on the assumption that the shortest amino acid sequence corresponds to a single domain.
ProDom hosts a comprehensive database of protein domain families. These domain families are automatically generated from global comparisons of all available protein sequences in the UniProt Knowledge Database.