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antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters
TLDR
We present the third version of antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, which has undergone major improvements. Expand
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antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification
TLDR
We present the thoroughly updated antiSMASH version 4, which adds several novel features, including prediction of gene cluster boundaries using ClusterFinder method or the newly integrated CASSIS algorithm, improved substrate specificity prediction for non-ribosomal peptide synthetase adenylation domains based on the new SANDPUMA algorithm and a domain-level alignment tool for comparative analysis of trans-AT polyketide synthase assembly line architectures. Expand
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antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences
TLDR
We present antiSMASH (antibiotics & Secondary Metabolite Analysis Shell), the first comprehensive pipeline capable of identifying biosynthetic loci covering the whole range of known secondary metabolite compound classes (polyketides, non-ribosomal peptides, terpenes, aminoglycosides and aminocoumarins). Expand
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antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline
Abstract Secondary metabolites produced by bacteria and fungi are an important source of antimicrobials and other bioactive compounds. In recent years, genome mining has seen broad applications inExpand
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antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers
TLDR
We present the highly improved antiSMASH 2.0 release, available at http://antismash.secondarymetabolites.org/. Expand
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NRPSpredictor2—a web server for predicting NRPS adenylation domain specificity
TLDR
We present an improved predictor, based on previous work (NRPSpredictor), that predicts A-domain specificity using Support Vector Machines on four hierarchical levels, ranging from gross physicochemical properties of an A- domain’s substrates down to single amino acid substrates. Expand
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Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs)
We present a new support vector machine (SVM)-based approach to predict the substrate specificity of subtypes of a given protein sequence family. We demonstrate the usefulness of this method on theExpand
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Phylogenetic analysis of condensation domains in NRPS sheds light on their functional evolution
BackgroundNon-ribosomal peptide synthetases (NRPSs) are large multimodular enzymes that synthesize a wide range of biologically active natural peptide compounds, of which many are pharmacologicallyExpand
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Minimum Information about a Biosynthetic Gene cluster.
A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters,Expand
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CRISPR-Cas9 Based Engineering of Actinomycetal Genomes.
Bacteria of the order Actinomycetales are one of the most important sources of pharmacologically active and industrially relevant secondary metabolites. Unfortunately, many of them are stillExpand
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