The ARTS toolset: Resistance-based genome mining for systematic prioritization of bioactive gene clusters

Natural products, especially those produced by bacteria and fungi, have been a rich source of antibiotics and other medically important compounds. Advances in genome sequencing have revealed that many microorganisms harbor far more biosynthetic potential than previously known, but identifying which gene clusters are most likely to produce bioactive compounds remains a major challenge. One promising strategy is to look for genes that protect the producing organism from its own toxic products-so-called resistance genes-which often appear near the biosynthetic genes. In this chapter, we introduce the ARTS toolset, a collection of computational tools designed to identify such resistance-linked biosynthetic gene clusters in microbial genomes. ARTS 2.0 allows users to analyze bacterial genomes and metagenomes, ARTS-DB provides access to precomputed results from tens of thousands of genomes, and FunARTS adapts the approach for fungal genomes. We describe how each tool works and provide examples to guide their use, with additional online tutorial videos provided by the authors.