The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark.
German Centre for Infection Research (DZIF), Interfaculty Institute of Microbiology and Infection Medicine, Auf der Morgenstelle 28, University of Tübingen, 72076 Tübingen, DE, Germany.
Nucleic Acids Res. 2019 Jul 2;47(W1):W81-W87. doi: 10.1093/nar/gkz310.
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.
细菌和真菌产生的次生代谢产物是抗菌剂和其他生物活性化合物的重要来源。近年来，基因组挖掘在识别和表征新化合物以及代谢工程方面得到了广泛应用。自 2011 年以来，“抗生素和次生代谢产物分析外壳-antiSMASH”（https://antismash.secondarymetabolites.org）一直作为一个网络服务器和独立工具，协助研究人员进行这方面的工作。它已经成为识别和分析细菌和真菌基因组序列中生物合成基因簇（BGCs）的最广泛使用的工具。在这里，我们展示了一个全新设计和扩展的 antiSMASH 版本 5。antiSMASH 5 添加了用于检测编码酰-氨基酸、β-内酰胺、真菌 RiPPs、RaS-RiPPs、多溴二苯醚、C-核苷、PPY 样酮和脂兰宁生物合成簇的检测规则。对于 II 型聚酮合酶编码基因簇，antiSMASH 5 现在提供了更详细的预测。HTML 输出可视化已重新设计，以改善注释的导航和视觉表示。我们再次提高了分析步骤的运行时间，使得在几分钟内为细菌基因组提供全面注释成为可能。一个新的以标准 JavaScript 对象表示法（JSON）格式输出的文件旨在为以编程方式处理 antiSMASH 结果的下游工具提供服务。
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