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Journal Article

antiSMASH 3.0––a comprehensive resource for the genome mining of biosynthetic gene clusters

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Medema,  Marnix H.
Microbial Genomics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Citation

Weber, T., Blin, K., Duddela, S., Krug, D., Kim, H. U., Bruccoleri, R., et al. (2015). antiSMASH 3.0––a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Research (London), 43: 1, pp. 1-7.


Cite as: https://hdl.handle.net/21.11116/0000-0001-C435-6
Abstract
Microbial secondary metabolism constitutes a rich
source of antibiotics, chemotherapeutics, insecti-
cides and other high-value chemicals. Genome min-
ing 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 un-
dergone 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 mod-
ule now identifies similarities of identified clusters
to any of 1172 clusters with known end products. At
the enzyme level, active sites of key biosynthetic en-
zymes are now pinpointed through a curated pattern-
matching procedure and Enzyme Commission num-
bers are assigned to functionally classify all enzyme-
coding genes. Additionally, chemical structure pre-
diction has been improved by incorporating polyke-
tide 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 mod-
ule allows offline editing of antiSMASH annotations
within the Geneious software.