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Nucleic Acids Res. 2019 Jul 2;47(W1):W81-W87. doi: 10.1093/nar/gkz310.

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline.

Author information

1
The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark.
2
German Centre for Infection Research (DZIF), Interfaculty Institute of Microbiology and Infection Medicine, Auf der Morgenstelle 28, University of Tübingen, 72076 Tübingen, DE, Germany.
3
Department of Chemical and Biomolecular Engineering (BK21 Plus Program) and BioInformatics Research Center, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea.
4
Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, the Netherlands.

Abstract

Secondary metabolites produced by bacteria and fungi are an important source of antimicrobials and other bioactive compounds. In recent years, genome mining has seen broad applications in identifying and characterizing new compounds as well as in metabolic engineering. Since 2011, the 'antibiotics and secondary metabolite analysis shell-antiSMASH' (https://antismash.secondarymetabolites.org) has assisted researchers in this, both as a web server and a standalone tool. It has established itself as the most widely used tool for identifying and analysing biosynthetic gene clusters (BGCs) in bacterial and fungal genome sequences. Here, we present an entirely redesigned and extended version 5 of antiSMASH. antiSMASH 5 adds detection rules for clusters encoding the biosynthesis of acyl-amino acids, β-lactones, fungal RiPPs, RaS-RiPPs, polybrominated diphenyl ethers, C-nucleosides, PPY-like ketones and lipolanthines. For type II polyketide synthase-encoding gene clusters, antiSMASH 5 now offers more detailed predictions. The HTML output visualization has been redesigned to improve the navigation and visual representation of annotations. We have again improved the runtime of analysis steps, making it possible to deliver comprehensive annotations for bacterial genomes within a few minutes. A new output file in the standard JavaScript object notation (JSON) format is aimed at downstream tools that process antiSMASH results programmatically.

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