{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T20:37:16Z","timestamp":1778704636359,"version":"3.51.4"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2021,5,12]],"date-time":"2021-05-12T00:00:00Z","timestamp":1620777600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Foundation","doi-asserted-by":"publisher","award":["NNF20CC0035580"],"award-info":[{"award-number":["NNF20CC0035580"]}],"id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Foundation","doi-asserted-by":"publisher","award":["NNF16OC0021746"],"award-info":[{"award-number":["NNF16OC0021746"]}],"id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001732","name":"Danish National Research Foundation","doi-asserted-by":"publisher","award":["DNRF137"],"award-info":[{"award-number":["DNRF137"]}],"id":[{"id":"10.13039\/501100001732","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"ERC","doi-asserted-by":"publisher","award":["948770-DECIPHER"],"award-info":[{"award-number":["948770-DECIPHER"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Netherlands Organization for Scientific Research","award":["731.014.206"],"award-info":[{"award-number":["731.014.206"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Many microorganisms produce natural products that form the basis of antimicrobials, antivirals, and other drugs. Genome mining is routinely used to complement screening-based workflows to discover novel natural products. Since 2011, the \"antibiotics and secondary metabolite analysis shell\u2014antiSMASH\" (https:\/\/antismash.secondarymetabolites.org\/) has supported researchers in their microbial genome mining tasks, both as a free-to-use web server and as a standalone tool under an OSI-approved open-source license. It is currently the most widely used tool for detecting and characterising biosynthetic gene clusters (BGCs) in bacteria and fungi. Here, we present the updated version 6 of antiSMASH. antiSMASH 6 increases the number of supported cluster types from 58 to 71, displays the modular structure of multi-modular BGCs, adds a new BGC comparison algorithm, allows for the integration of results from other prediction tools, and more effectively detects tailoring enzymes in RiPP clusters.<\/jats:p>","DOI":"10.1093\/nar\/gkab335","type":"journal-article","created":{"date-parts":[[2021,4,19]],"date-time":"2021-04-19T18:31:51Z","timestamp":1618857111000},"page":"W29-W35","source":"Crossref","is-referenced-by-count":2422,"title":["antiSMASH 6.0: improving cluster detection and comparison capabilities"],"prefix":"10.1093","volume":"49","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3764-6051","authenticated-orcid":false,"given":"Kai","family":"Blin","sequence":"first","affiliation":[{"name":"The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark"}]},{"given":"Simon","family":"Shaw","sequence":"additional","affiliation":[{"name":"The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark"}]},{"given":"Alexander M","family":"Kloosterman","sequence":"additional","affiliation":[{"name":"Institute of Biology, Leiden University, Leiden, The Netherlands"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8816-4680","authenticated-orcid":false,"given":"Zach","family":"Charlop-Powers","sequence":"additional","affiliation":[{"name":"Bioinformatics, Lodo Therapeutics, New York, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0341-1561","authenticated-orcid":false,"given":"Gilles P","family":"van\u00a0Wezel","sequence":"additional","affiliation":[{"name":"Institute of Biology, Leiden University, Leiden, The Netherlands"},{"name":"Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2191-2821","authenticated-orcid":false,"given":"Marnix\u00a0H","family":"Medema","sequence":"additional","affiliation":[{"name":"Institute of Biology, Leiden University, Leiden, The Netherlands"},{"name":"Bioinformatics Group, Wageningen University, Wageningen, The Netherlands"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8260-5120","authenticated-orcid":false,"given":"Tilmann","family":"Weber","sequence":"additional","affiliation":[{"name":"The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark"}]}],"member":"286","published-online":{"date-parts":[[2021,5,12]]},"reference":[{"key":"2021070812071566200_B1","doi-asserted-by":"crossref","first-page":"770","DOI":"10.1021\/acs.jnatprod.9b01285","article-title":"Natural products as sources of new drugs over the nearly four decades from 01\/1981 to 09\/2019","volume":"83","author":"Newman","year":"2020","journal-title":"J. Nat. Prod."},{"key":"2021070812071566200_B2","doi-asserted-by":"crossref","first-page":"988","DOI":"10.1039\/C6NP00025H","article-title":"The evolution of genome mining in microbes - a review","volume":"33","author":"Ziemert","year":"2016","journal-title":"Nat. Prod. Rep."},{"key":"2021070812071566200_B3","doi-asserted-by":"crossref","first-page":"W278","DOI":"10.1093\/nar\/gky383","article-title":"BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins","volume":"46","author":"van\u00a0Heel","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2021070812071566200_B4","doi-asserted-by":"crossref","first-page":"6058","DOI":"10.1038\/s41467-020-19986-1","article-title":"Comprehensive prediction of secondary metabolite structure and biological activity from microbial genome sequences","volume":"11","author":"Skinnider","year":"2020","journal-title":"Nat. Commun."},{"key":"2021070812071566200_B5","doi-asserted-by":"crossref","first-page":"4624","DOI":"10.1093\/nar\/gkz192","article-title":"Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool","volume":"47","author":"Santos-Aberturas","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2021070812071566200_B6","doi-asserted-by":"crossref","first-page":"lqaa098","DOI":"10.1093\/nargab\/lqaa098","article-title":"TOUCAN: a framework for fungal biosynthetic gene cluster discovery","volume":"2","author":"Almeida","year":"2020","journal-title":"NAR Genom Bioinform"},{"key":"2021070812071566200_B7","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1016\/j.ijmm.2014.02.001","article-title":"In silico tools for the analysis of antibiotic biosynthetic pathways","volume":"304","author":"Weber","year":"2014","journal-title":"Int. J. Med. Microbiol."},{"key":"2021070812071566200_B8","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1038\/nchembio.1884","article-title":"Computational approaches to natural product discovery","volume":"11","author":"Medema","year":"2015","journal-title":"Nat. Chem. Biol."},{"key":"2021070812071566200_B9","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1016\/j.synbio.2015.12.002","article-title":"The secondary metabolite bioinformatics portal: computational tools to facilitate synthetic biology of secondary metabolite production","volume":"1","author":"Weber","year":"2016","journal-title":"Synth Syst Biotechnol"},{"key":"2021070812071566200_B10","doi-asserted-by":"crossref","first-page":"1103","DOI":"10.1093\/bib\/bbx146","article-title":"Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters","volume":"20","author":"Blin","year":"2019","journal-title":"Brief. Bioinform."},{"key":"2021070812071566200_B11","doi-asserted-by":"crossref","first-page":"W339","DOI":"10.1093\/nar\/gkr466","article-title":"antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences","volume":"39","author":"Medema","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2021070812071566200_B12","doi-asserted-by":"crossref","first-page":"W204","DOI":"10.1093\/nar\/gkt449","article-title":"antiSMASH 2.0\u2013a versatile platform for genome mining of secondary metabolite producers","volume":"41","author":"Blin","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2021070812071566200_B13","doi-asserted-by":"crossref","first-page":"W237","DOI":"10.1093\/nar\/gkv437","article-title":"antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters","volume":"43","author":"Weber","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2021070812071566200_B14","doi-asserted-by":"crossref","first-page":"W36","DOI":"10.1093\/nar\/gkx319","article-title":"antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification","volume":"45","author":"Blin","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2021070812071566200_B15","doi-asserted-by":"crossref","first-page":"W81","DOI":"10.1093\/nar\/gkz310","article-title":"antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline","volume":"47","author":"Blin","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2021070812071566200_B16","doi-asserted-by":"crossref","first-page":"W546","DOI":"10.1093\/nar\/gkaa374","article-title":"ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining","volume":"48","author":"Mungan","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2021070812071566200_B17","doi-asserted-by":"crossref","first-page":"e1003822","DOI":"10.1371\/journal.pcbi.1003822","article-title":"Pep2Path: automated mass spectrometry-guided genome mining of peptidic natural products","volume":"10","author":"Medema","year":"2014","journal-title":"PLoS Comput. Biol."},{"key":"2021070812071566200_B18","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.synbio.2020.05.005","article-title":"Designing sgRNAs for CRISPR-BEST base editing applications with CRISPy-web 2.0","volume":"5","author":"Blin","year":"2020","journal-title":"Synth Syst Biotechnol"},{"key":"2021070812071566200_B19","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1038\/s41589-019-0400-9","article-title":"A computational framework to explore large-scale biosynthetic diversity","volume":"16","author":"Navarro-Mu\u00f1oz","year":"2020","journal-title":"Nat. Chem. Biol."},{"key":"2021070812071566200_B20","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giaa154","article-title":"BiG-SLiCE: a highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters","volume":"10","author":"Kautsar","year":"2021","journal-title":"Gigascience"},{"key":"2021070812071566200_B21","first-page":"D422","article-title":"IMG-ABC v.5.0: an update to the IMG\/Atlas of Biosynthetic Gene Clusters Knowledgebase","volume":"48","author":"Palaniappan","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2021070812071566200_B22","first-page":"D579","article-title":"MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis","volume":"48","author":"Vallenet","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2021070812071566200_B23","first-page":"D454","article-title":"MIBiG 2.0: a repository for biosynthetic gene clusters of known function","volume":"48","author":"Kautsar","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2021070812071566200_B24","doi-asserted-by":"crossref","first-page":"D490","DOI":"10.1093\/nar\/gkaa812","article-title":"BiG-FAM: the biosynthetic gene cluster families database","volume":"49","author":"Kautsar","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2021070812071566200_B25","doi-asserted-by":"crossref","first-page":"D639","DOI":"10.1093\/nar\/gkaa978","article-title":"The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes","volume":"49","author":"Blin","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2021070812071566200_B26","doi-asserted-by":"crossref","first-page":"D412","DOI":"10.1093\/nar\/gkaa913","article-title":"Pfam: the protein families database in 2021","volume":"49","author":"Mistry","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2021070812071566200_B27","doi-asserted-by":"crossref","first-page":"D387","DOI":"10.1093\/nar\/gks1234","article-title":"TIGRFAMs and genome properties in 2013","volume":"41","author":"Haft","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2021070812071566200_B28","doi-asserted-by":"crossref","first-page":"D458","DOI":"10.1093\/nar\/gkaa937","article-title":"SMART: recent updates, new developments and status in 2020","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2021070812071566200_B29","doi-asserted-by":"crossref","first-page":"e1000351","DOI":"10.1371\/journal.pcbi.1000351","article-title":"Towards prediction of metabolic products of polyketide synthases: an in silico analysis","volume":"5","author":"Yadav","year":"2009","journal-title":"PLoS Comput. 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Biotechnol."},{"key":"2021070812071566200_B36","doi-asserted-by":"crossref","first-page":"e00267-20","DOI":"10.1128\/mSystems.00267-20","article-title":"RRE-Finder: a genome-mining tool for class-independent RiPP discovery","volume":"5","author":"Kloosterman","year":"2020","journal-title":"mSystems"},{"key":"2021070812071566200_B37","doi-asserted-by":"crossref","first-page":"3297","DOI":"10.1039\/D0CS00162G","article-title":"Linking genomics and metabolomics to chart specialized metabolic diversity","volume":"49","author":"van\u00a0der\u00a0Hooft","year":"2020","journal-title":"Chem. Soc. Rev."},{"key":"2021070812071566200_B38","doi-asserted-by":"crossref","first-page":"828","DOI":"10.1038\/nbt.3597","article-title":"Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking","volume":"34","author":"Wang","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"2021070812071566200_B39","doi-asserted-by":"crossref","first-page":"1501","DOI":"10.1046\/j.1365-2958.2003.03523.x","article-title":"The large linear plasmid pSLA2-L of Streptomyces rochei has an unusually condensed gene organization for secondary metabolism","volume":"48","author":"Mochizuki","year":"2003","journal-title":"Mol. Microbiol."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/49\/W1\/W29\/38841738\/gkab335.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/49\/W1\/W29\/38841738\/gkab335.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,7,8]],"date-time":"2021-07-08T17:07:58Z","timestamp":1625764078000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/49\/W1\/W29\/6274535"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,5,12]]},"references-count":39,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2021,5,12]]},"published-print":{"date-parts":[[2021,7,2]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkab335","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.740104003.793586204","asserted-by":"object"}]},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,7,2]]},"published":{"date-parts":[[2021,5,12]]}}}