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

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ID: 3525
2019
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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.
Reference Key
blin2019antismashnucleic Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Blin, Kai;Shaw, Simon;Steinke, Katharina;Villebro, Rasmus;Ziemert, Nadine;Lee, Sang Yup;Medema, Marnix H;Weber, Tilmann;
Journal Nucleic Acids Research
Year 2019
DOI
10.1093/nar/gkz310
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