antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters.
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Kim, Hyun Uk
Lee, Sang Yup
Fischbach, Michael A
Medema, Marnix H
MetadataShow full item record
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.
CitationantiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. 2015: Nucleic Acids Res.
AffiliationHelmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarland University, Saarbrucken, Germany.
JournalNucleic acids research
The following license files are associated with this item:
- antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers.
- Authors: Blin K, Medema MH, Kazempour D, Fischbach MA, Breitling R, Takano E, Weber T
- Issue date: 2013 Jul
- Sequence-based classification of type II polyketide synthase biosynthetic gene clusters for antiSMASH.
- Authors: Villebro R, Shaw S, Blin K, Weber T
- Issue date: 2019 Mar
- antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.
- Authors: Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA, Weber T, Takano E, Breitling R
- Issue date: 2011 Jul
- antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline.
- Authors: Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, Medema MH, Weber T
- Issue date: 2019 Jul 2
- antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification.
- Authors: Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ, Kautsar SA, Suarez Duran HG, de Los Santos ELC, Kim HU, Nave M, Dickschat JS, Mitchell DA, Shelest E, Breitling R, Takano E, Lee SY, Weber T, Medema MH
- Issue date: 2017 Jul 3