Introduction

The secondary metabolism of bacteria and fungi constitutes a rich source of bioactive compounds of potential pharmaceutical value, comprising biosynthetic pathways of many chemicals that have been and are being utilized as e.g. antibiotics, cholesterol-lowering drugs or antitumor drugs. Interestingly, the genes encoding the biosynthetic pathway responsible for the production of such a secondary metabolite are very often spatially clustered together at a certain position on the chromosome; such a compendium of genes is referred to as a 'secondary metabolite biosynthesis gene cluster'. This genetic architecture has opened up the possibility for straightforward detection of secondary metabolite biosynthesis pathways by locating their gene clusters. In recent years, the costs of sequencing bacterial and fungi has dropped dramatically, and many genome sequences have become available. Based on profile hidden Markov models of genes that are specific for certain types of gene clusters, antiSMASH is able to accurately identify the gene clusters encoding secondary metabolites of all known broad chemical classes. antiSMASH not only detects the gene clusters, but also offers detailed sequence analysis.