CASSIS ("cluster assignment by islands of sites") is a tool to predict secondary metabolite gene clusters around a given anchor/backbone gene. A gene cluster is a small group of genes, which are tightly co-localized, co-regulated, and participate in the same metabolic pathway.
CASSIS utilizes a so-called "motif-based" prediction method. It is mainly based on the hypothesized co-regulation of cluster genes. Hence, CASSIS searches for transcription factor binding sites shared by promoter sequences of putative cluster genes.
SMIPS ("secondary metabolites by InterProScan") is a tool for genome-wide prediction of anchor/backbone genes. Anchor genes encode enzymes, which play a major role in the biosynthesis of secondary metabolites. SMIPS identifies three most common classes of the anchor genes: polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), and dimethylallyltryptophan synthases (DMATS).
The anchor gene predictions made by SMIPS are based on protein domain annotations provided by the InterProScan tool.