Figure 2.

General Workflow of antiSMASH

Primarily, antiSMASH identifies signature biosynthetic genes (hit on their pHMMs) that encode enzymes responsible for generating a class-specific scaffold and locates a cluster based on a set of manually curated BGC cluster rules. Alternatively, it uses the ClusterFinder algorithm for BGC prediction. For fungal BGCs, Cluster Assignment by Islands of Sites (CASSIS) is integrated for better prediction of gene cluster boundaries. In addition, several downstream analyses can be performed: NRPS/PKS domain analysis and annotation, prediction of the core chemical structure of PKSs and NRPSs, substrate specificity prediction for NRPS ‘A’ domains (via NRPSpredictor2) (Röttig et al., 2011), ClusterBlast gene cluster comparative analysis, and smCOG secondary metabolism protein family analysis.