antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

By Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber, Eriko Takano, Rainer Breitling. Nucleic Acids Res., 2011

1,865 citations recorded by the source corpus.

Bacterial and fungal secondary metabolism is a rich source of novel bioactive compounds with potential pharmaceutical applications as antibiotics, anti-tumor drugs or cholesterol-lowering drugs. To find new drug candidates, microbiologists are increasingly relying on sequencing genomes of a wide variety of microbes. However, rapidly and reliably pinpointing all the potential gene clusters for secondary metabolites in dozens of newly sequenced genomes has been extremely challenging, due to their biochemical heterogeneity, the presence of unknown enzymes and the dispersed nature of the necessary specialized bioinformatics tools and resources. Here, we present antiSMASH (antibiotics & Secondary Metabolite Analysis Shell), the first comprehensive pipeline capable of identifying biosynthetic loci covering the whole range of known secondary metabolite compound classes (polyketides, non-ribosomal peptides, terpenes, aminoglycosides, aminocoumarins, indolocarbazoles, lantibiotics, bacteriocins, nucleosides, beta-lactams, butyrolactones, siderophores, melanins and others). It aligns the identified regions at the gene cluster level to their nearest relatives from a database containing all other known gene clusters, and integrates or cross-links all previously available secondary-metabolite specific gene analysis methods in one interactive view. antiSMASH is available at http://antismash.secondarymetabolites.org.

Subfields: Biotechnology, Molecular Biology, Pharmacology

View Paper: https://www.semanticscholar.org/paper/e2a4073a235cd58a67be0eeae9b415c8426b468c

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Citations in the corpus

antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation (2023, positive): “Since its 2011 release, antiSMASH ( 8–13 ) has established itself as the most widely used tool for mining microbial genomes for SM BGCs.”
antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers (2013, methodology): “…the ﬁrst version of the ‘antibiotics and secondary metabolite analysis shell’ (antiSMASH), a web server and stand-alone software, which combines automated identiﬁcation of secondary metabolite gene clusters in genome sequences with a large collection of compound-speciﬁc analysis algorithms (17).”
Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions (2012, methodology): “Secondary metabolite production clusters were examined using the antiSMASH program [147].”
An Overview on Marine Sponge-Symbiotic Bacteria as Unexhausted Sources for Natural Product Discovery (2017, methodology): “One widely used computational tool used to identify these cryptic biosynthetic gene clusters is antiSMASH (antibiotics and secondary metabolite analysis shell) [227] which allows the input of multiple related sequences, direct analysis of protein sequences, and detection of added classes of speciali”
Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. (2014, methodology): “1Department of Bioengineering and Therapeutic Sciences and the California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA 2Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Gron”
antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters (2015, methodology): “Since 2011, the antibiotics and SecondaryMetabolite Analysis SHell (antiSMASH) has served as a comprehensive web server and a stand-alone tool for the automatic genomic identi cation and analysis of BGCs of any type, thus facilitating rapid genomemining of a wide range of bacterial and fungal strain”
Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing (2012, methodology): “ters were identified using met2db (39), antiSMASH (40), and NaPDoS (41).”
antiSMASH 6.0: improving cluster detection and comparison capabilities (2021, background): “Since its initial release in 2011, antiSMASH (11–15) has become the most widely used tool for mining microbial genomes for secondary / specialised metabolite (SM) biosynthetic gene clusters (BGCs) and is regarded as the gold standard.”