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

M. H. Medema, K. Blin, P. Cimermancic, V. de Jager, P. Zakrzewski, M. A. Fischbach, Tilmann Weber, E. Takano, R. Breitling

Research output: Contribution to journalJournal articleResearchpeer-review

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.
Original languageEnglish
JournalNucleic acids research
Volume39
Pages (from-to)W339-W346
ISSN1362-4962
DOIs
Publication statusPublished - 2011
Externally publishedYes

Keywords

  • Bacteria/enzymology/genetics/*metabolism Biosynthetic Pathways/genetics Fungi/enzymology/genetics/*metabolism *Genes, Bacterial *Genes, Fungal Genome, Bacterial Genome, Fungal Genomics Internet Molecular Sequence Annotation Peptide Synthases/chemistry Polyketide Synthases/chemistry *Software Substrate Specificity

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