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- Title
CASSIS and SMIPS: promoter-based prediction of secondary metabolite gene clusters in eukaryotic genomes.
- Authors
Wolf, Thomas; Shelest, Vladimir; Nath, Neetika; Shelest, Ekaterina
- Abstract
Motivation: Secondary metabolites (SM) are structurally diverse natural products of high pharmaceutical importance. Genes involved in their biosynthesis are often organized in clusters, i.e., are co-localized and co-expressed. In silico cluster prediction in eukaryotic genomes remains problematic mainly due to the high variability of the clusters content and lack of other distinguishing sequence features. Results: We present Cluster Assignment by Islands of Sites (CASSIS), a method for SM cluster prediction in eukaryotic genomes, and Secondary Metabolites by InterProScan (SMIPS), a tool for genome-wide detection of SM key enzymes ('anchor' genes): polyketide synthases, non-ribosomal peptide synthetases and dimethylallyl tryptophan synthases. Unlike other tools based on protein similarity, CASSIS exploits the idea of co-regulation of the cluster genes, which assumes the existence of common regulatory patterns in the cluster promoters. The method searches for 'islands' of enriched cluster-specific motifs in the vicinity of anchor genes. It was validated in a series of crossvalidation experiments and showed high sensitivity and specificity. Availability and implementation: CASSIS and SMIPS are freely available at https://sbi.hki-jena.de/cassis.
- Subjects
METABOLITES; GENES; BIOSYNTHESIS; GENOMES; CHEMICAL synthesis; POLYKETIDES; MATHEMATICAL models
- Publication
Bioinformatics, 2016, Vol 32, Issue 8, p1138
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btv713