2.50
Hdl Handle:
http://hdl.handle.net/10033/555475
Title:
antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters.
Authors:
Weber, Tilmann; Blin, Kai; Duddela, Srikanth; Krug, Daniel; Kim, Hyun Uk; Bruccoleri, Robert; Lee, Sang Yup; Fischbach, Michael A; Müller, Rolf; Wohlleben, Wolfgang; Breitling, Rainer; Takano, Eriko; Medema, Marnix H
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.
Affiliation:
Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarland University, Saarbrucken, Germany.
Citation:
antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. 2015: Nucleic Acids Res.
Journal:
Nucleic acids research
Issue Date:
6-May-2015
URI:
http://hdl.handle.net/10033/555475
DOI:
10.1093/nar/gkv437
PubMed ID:
25948579
Type:
Article
ISSN:
1362-4962
Appears in Collections:
publications of the department of microbial natural substances ([HIPS]MINS)

Full metadata record

DC FieldValue Language
dc.contributor.authorWeber, Tilmannen
dc.contributor.authorBlin, Kaien
dc.contributor.authorDuddela, Srikanthen
dc.contributor.authorKrug, Danielen
dc.contributor.authorKim, Hyun Uken
dc.contributor.authorBruccoleri, Roberten
dc.contributor.authorLee, Sang Yupen
dc.contributor.authorFischbach, Michael Aen
dc.contributor.authorMüller, Rolfen
dc.contributor.authorWohlleben, Wolfgangen
dc.contributor.authorBreitling, Raineren
dc.contributor.authorTakano, Erikoen
dc.contributor.authorMedema, Marnix Hen
dc.date.accessioned2015-05-22T14:32:00Zen
dc.date.available2015-05-22T14:32:00Zen
dc.date.issued2015-05-06en
dc.identifier.citationantiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. 2015: Nucleic Acids Res.en
dc.identifier.issn1362-4962en
dc.identifier.pmid25948579en
dc.identifier.doi10.1093/nar/gkv437en
dc.identifier.urihttp://hdl.handle.net/10033/555475en
dc.description.abstractMicrobial 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.en
dc.languageENGen
dc.titleantiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters.en
dc.typeArticleen
dc.contributor.departmentHelmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarland University, Saarbrucken, Germany.en
dc.identifier.journalNucleic acids researchen

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