title: antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters.
abstract: Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. In 2011, we introduced antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.secondarymetabolites.org. Here, we present version 3.0 of antiSMASH, which has undergone major improvements. A full integration of the recently published ClusterFinder algorithm now allows using this probabilistic algorithm to detect putative gene clusters of unknown types. Also, a new dereplication variant of the ClusterBlast module now identifies similarities of identified clusters to any of 1172 clusters with known end products. At the enzyme level, active sites of key biosynthetic enzymes are now pinpointed through a curated pattern-matching procedure and Enzyme Commission numbers are assigned to functionally classify all enzyme-coding genes. Additionally, chemical structure prediction has been improved by incorporating polyketide reduction states. Finally, in order for users to be able to organize and analyze multiple antiSMASH outputs in a private setting, a new XML output module allows offline editing of antiSMASH annotations within the Geneious software.
authors.affiliation: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark marnix.medema@wur.nl.
authors.forename: Tilmann
authors.initials: T
authors.lastname: Weber
authors.affiliation: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark.
authors.forename: Kai
authors.initials: K
authors.lastname: Blin
authors.affiliation: Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarland University, Saarbrücken, Germany.
authors.forename: Srikanth
authors.initials: S
authors.lastname: Duddela
authors.affiliation: Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarland University, Saarbrücken, Germany German Centre for Infection Research (DZIF), Location Hannover-Braunschweig, Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Krug
authors.affiliation: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark Department of Chemical and Biomolecular Engineering (BK21 Plus Program) / BioInformatics Research Center, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.
authors.forename: Hyun Uk
authors.initials: HU
authors.lastname: Kim
authors.affiliation: Congenomics, LLC, Glastonbury, CT, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Bruccoleri
authors.affiliation: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark Department of Chemical and Biomolecular Engineering (BK21 Plus Program) / BioInformatics Research Center, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.
authors.forename: Sang Yup
authors.initials: SY
authors.lastname: Lee
authors.affiliation: Department of Bioengineering and Therapeutic Sciences/California Institute for Quantitative Biosciences, University of California, San Francisco, USA.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Fischbach
authors.affiliation: Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarland University, Saarbrücken, Germany German Centre for Infection Research (DZIF), Location Hannover-Braunschweig, Germany.
authors.forename: Rolf
authors.initials: R
authors.lastname: Müller
authors.affiliation: Interfaculty Institute for Microbiology and Infection Medicine, Eberhard Karls University of Tübingen, Tübingen, Germany German Center for Infection Research (DZIF), Location Tübingen, Germany.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Wohlleben
authors.affiliation: Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, The University of Manchester, Manchester, UK.
authors.forename: Rainer
authors.initials: R
authors.lastname: Breitling
authors.affiliation: Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, The University of Manchester, Manchester, UK.
authors.forename: Eriko
authors.initials: E
authors.lastname: Takano
authors.affiliation: Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany Bioinformatics Group, Wageningen University, Wageningen, The Netherlands marnix.medema@wur.nl.
authors.forename: Marnix H
authors.initials: MH
authors.lastname: Medema
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000235:genetics* / Q000378:metabolism; D053898:Biosynthetic Pathways / Q000235:genetics; D020134:Catalytic Domain; D057225:Data Mining; D004798:Enzymes / Q000737:chemistry; D005658:Fungi / Q000235:genetics* / Q000378:metabolism; D023281:Genomics / Q000379:methods; D020407:Internet; D061065:Polyketides; D064210:Secondary Metabolism / Q000235:genetics*; D012984:Software
chemical_list: D004798:Enzymes; D061065:Polyketides