{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,27]],"date-time":"2026-04-27T13:17:24Z","timestamp":1777295844076,"version":"3.51.4"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2020,10,3]],"date-time":"2020-10-03T00:00:00Z","timestamp":1601683200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Graduate School for Experimental Plant Sciences"},{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Foundation","doi-asserted-by":"publisher","award":["NNF10CC1016517"],"award-info":[{"award-number":["NNF10CC1016517"]}],"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"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Computational analysis of biosynthetic gene clusters (BGCs) has revolutionized natural product discovery by enabling the rapid investigation of secondary metabolic potential within microbial genome sequences. Grouping homologous BGCs into Gene Cluster Families (GCFs) facilitates mapping their architectural and taxonomic diversity and provides insights into the novelty of putative BGCs, through dereplication with BGCs of known function. While multiple databases exist for exploring BGCs from publicly available data, no public resources exist that focus on GCF relationships. Here, we present BiG-FAM, a database of 29,955 GCFs capturing the global diversity of 1,225,071 BGCs predicted from 209,206 publicly available microbial genomes and metagenome-assembled genomes (MAGs). The database offers rich functionalities, such as multi-criterion GCF searches, direct links to BGC databases such as antiSMASH-DB, and rapid GCF annotation of user-supplied BGCs from antiSMASH results. BiG-FAM can be accessed online at https:\/\/bigfam.bioinformatics.nl.<\/jats:p>","DOI":"10.1093\/nar\/gkaa812","type":"journal-article","created":{"date-parts":[[2020,9,16]],"date-time":"2020-09-16T15:47:49Z","timestamp":1600271269000},"page":"D490-D497","source":"Crossref","is-referenced-by-count":235,"title":["BiG-FAM: the biosynthetic gene cluster families database"],"prefix":"10.1093","volume":"49","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9815-511X","authenticated-orcid":false,"given":"Satria A","family":"Kautsar","sequence":"first","affiliation":[{"name":"Bioinformatics Group, Wageningen University, 6708PB Wageningen, The Netherlands"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3764-6051","authenticated-orcid":false,"given":"Kai","family":"Blin","sequence":"additional","affiliation":[{"name":"The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark"}]},{"given":"Simon","family":"Shaw","sequence":"additional","affiliation":[{"name":"The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark"}]},{"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, 2800 Kgs. Lyngby, Denmark"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2191-2821","authenticated-orcid":false,"given":"Marnix H","family":"Medema","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Wageningen University, 6708PB Wageningen, The Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2020,10,3]]},"reference":[{"key":"2021010313124952800_B1","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1007\/s10295-013-1325-z","article-title":"Importance of microbial natural products and the need to revitalize their discovery","volume":"41","author":"Demain","year":"2014","journal-title":"J. Ind. Microbiol. Biotechnol."},{"key":"2021010313124952800_B2","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1046\/j.1469-0691.2003.00489.x","article-title":"Microbial natural products as a source of antifungals","volume":"9","author":"Vicente","year":"2003","journal-title":"Clin. Microbiol. Infect."},{"key":"2021010313124952800_B3","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":"2021010313124952800_B4","doi-asserted-by":"crossref","first-page":"W49","DOI":"10.1093\/nar\/gkx320","article-title":"PRISM 3: expanded prediction of natural product chemical structures from microbial genomes","volume":"45","author":"Skinnider","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2021010313124952800_B5","doi-asserted-by":"crossref","first-page":"D625","DOI":"10.1093\/nar\/gky1060","article-title":"The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters","volume":"47","author":"Blin","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2021010313124952800_B6","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":"2021010313124952800_B7","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":"2021010313124952800_B8","doi-asserted-by":"crossref","first-page":"1218","DOI":"10.1093\/molbev\/mst025","article-title":"Detecting sequence homology at the gene cluster level with MultiGeneBlast","volume":"30","author":"Medema","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"2021010313124952800_B9","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1186\/1471-2164-14-611","article-title":"Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes","volume":"14","author":"Doroghazi","year":"2013","journal-title":"BMC Genomics"},{"key":"2021010313124952800_B10","doi-asserted-by":"crossref","first-page":"E1130","DOI":"10.1073\/pnas.1324161111","article-title":"Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora","volume":"111","author":"Ziemert","year":"2014","journal-title":"Proc. Natl. Acad. Sci. 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