title: antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.
abstract: 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.
authors.affiliation: Department of Microbial Physiology, Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands.
authors.forename: Marnix H
authors.initials: MH
authors.lastname: Medema
authors.forename: Kai
authors.initials: K
authors.lastname: Blin
authors.forename: Peter
authors.initials: P
authors.lastname: Cimermancic
authors.forename: Victor
authors.initials: V
authors.lastname: de Jager
authors.forename: Piotr
authors.initials: P
authors.lastname: Zakrzewski
authors.forename: Michael A
authors.initials: MA
authors.lastname: Fischbach
authors.forename: Tilmann
authors.initials: T
authors.lastname: Weber
authors.forename: Eriko
authors.initials: E
authors.lastname: Takano
authors.forename: Rainer
authors.initials: R
authors.lastname: Breitling
mesh_terms: D001419:Bacteria / Q000201:enzymology / Q000235:genetics / Q000378:metabolism*; D053898:Biosynthetic Pathways / Q000235:genetics; D005658:Fungi / Q000201:enzymology / Q000235:genetics / Q000378:metabolism*; D005798:Genes, Bacterial; D005800:Genes, Fungal; D016680:Genome, Bacterial; D016681:Genome, Fungal; D023281:Genomics; D020407:Internet; D058977:Molecular Sequence Annotation; D010453:Peptide Synthases / Q000737:chemistry; D048630:Polyketide Synthases / Q000737:chemistry; D012984:Software; D013379:Substrate Specificity
chemical_list: D048630:Polyketide Synthases; D010453:Peptide Synthases; C104385:non-ribosomal peptide synthase