{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T15:38:35Z","timestamp":1770997115892,"version":"3.50.1"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2016,10,12]],"date-time":"2016-10-12T00:00:00Z","timestamp":1476230400000},"content-version":"vor","delay-in-days":308,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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\u2019 content and lack of other distinguishing sequence features.<\/jats:p>\n               <jats:p>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 (\u2018anchor\u2019 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 \u2018islands\u2019 of enriched cluster-specific motifs in the vicinity of anchor genes. It was validated in a series of cross-validation experiments and showed high sensitivity and specificity.<\/jats:p>\n               <jats:p>Availability and implementation: CASSIS and SMIPS are freely available at https:\/\/sbi.hki-jena.de\/cassis.<\/jats:p>\n               <jats:p>Contact: \u00a0thomas.wolf@leibniz-hki.de or ekaterina.shelest@leibniz-hki.de<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv713","type":"journal-article","created":{"date-parts":[[2015,12,13]],"date-time":"2015-12-13T07:12:30Z","timestamp":1449990750000},"page":"1138-1143","source":"Crossref","is-referenced-by-count":114,"title":["CASSIS and SMIPS: promoter-based prediction of secondary metabolite gene clusters in eukaryotic genomes"],"prefix":"10.1093","volume":"32","author":[{"given":"Thomas","family":"Wolf","sequence":"first","affiliation":[{"name":"Research Group Systems Biology\/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology \u2013 Hans-Kn\u00f6ll-Institute (HKI), Jena 07745, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vladimir","family":"Shelest","sequence":"additional","affiliation":[{"name":"Research Group Systems Biology\/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology \u2013 Hans-Kn\u00f6ll-Institute (HKI), Jena 07745, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Neetika","family":"Nath","sequence":"additional","affiliation":[{"name":"Research Group Systems Biology\/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology \u2013 Hans-Kn\u00f6ll-Institute (HKI), Jena 07745, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ekaterina","family":"Shelest","sequence":"additional","affiliation":[{"name":"Research Group Systems Biology\/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology \u2013 Hans-Kn\u00f6ll-Institute (HKI), Jena 07745, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,12,9]]},"reference":[{"key":"2023020112011461200_btv713-B1","first-page":"107","volume-title":"Annual Review of Phytopathology.","author":"Amaike","year":"2011"},{"key":"2023020112011461200_btv713-B2","doi-asserted-by":"crossref","first-page":"E99","DOI":"10.1073\/pnas.1205532110","article-title":"Accurate prediction of secondary metabolite gene clusters in filamentous fungi","volume":"110","author":"Andersen","year":"2013","journal-title":"Proc. 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