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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.
