antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline
By Kai Blin, S. Shaw, Katharina Steinke, Rasmus Villebro, Nadine Ziemert, Sang Yup Lee, Marnix H. Medema, Tilmann Weber. Nucleic Acids Res., 2019
2,482 citations recorded by the source corpus.
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.
Subfields: Molecular Biology, Pharmacology
View Paper: https://www.semanticscholar.org/paper/3f9cb68785e92b6d39e99c9868244906980133fb
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In Molecular Biology
- Kai Blin
- Tilmann Weber
- Marnix H. Medema
- P. Bakker
- C. Pieterse
- C. Zamioudis
- Mohammad Alanjary
- Michael A. Fischbach
In Pharmacology
Citations in the corpus
- MIBiG 2.0: a repository for biosynthetic gene clusters of known function (2019, methodology): “Now, the MIBiG repository has become a central reference database for BGCs of known function, and provides the basis for comparative analyses in antiSMASH (1) via the KnownClusterBlast module.”
- Pseudomonas simiae WCS417: star track of a model beneficial rhizobacterium (2020, background): “…volatile organic compounds (VOCs) produced by WCS417 induced similar root architectural changes and enhanced the shoot fresh weight of Arabidopsis (Blom et al. 2011; Zamioudis et al. 2013), suggesting that stimulation of endogenous auxin responses byWCS417 VOCs plays a role in plant growth…”