CASSIS and SMIPS: promoter-based prediction of secondary metabolite gene clusters in eukaryotic genomes.

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 protei

SUBMITTER: Wolf T 

PROVIDER: S-EPMC4824125 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature