{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T18:42:56Z","timestamp":1675190576876},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Unraveling regulatory mechanisms (e.g. identification of motifs in cis-regulatory regions) remains a major challenge in the analysis of transcriptome experiments. Existing applications identify putative motifs from gene lists obtained at rather arbitrary cutoff and require additional manual processing steps. Our standalone application MOTIFATOR identifies the most optimal parameters for motif discovery and creates an interactive visualization of the results. Discovered putative motifs are functionally characterized, thereby providing valuable insight in the biological processes that could be controlled by the motif.<\/jats:p>\n               <jats:p>Availability: MOTIFATOR is freely available at http:\/\/www.motifator.nl<\/jats:p>\n               <jats:p>Contact: \u00a0o.p.kuipers@rug.nl; sacha.vanhijum@nizo.nl<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp013","type":"journal-article","created":{"date-parts":[[2009,1,26]],"date-time":"2009-01-26T01:13:06Z","timestamp":1232932386000},"page":"550-551","source":"Crossref","is-referenced-by-count":3,"title":["MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data"],"prefix":"10.1093","volume":"25","author":[{"given":"Evert-Jan","family":"Blom","sequence":"first","affiliation":[{"name":"1 Molecular Genetics, Groningen Biomolecular Sciences, University of Groningen, PO Box 800, 9700 AV and 2Institute for Mathematics and Computing Science, University of Groningen, Nijenborgh 9, 9747 AG, Groningen, The Netherlands"}]},{"given":"Jos B. T. M.","family":"Roerdink","sequence":"additional","affiliation":[{"name":"1 Molecular Genetics, Groningen Biomolecular Sciences, University of Groningen, PO Box 800, 9700 AV and 2Institute for Mathematics and Computing Science, University of Groningen, Nijenborgh 9, 9747 AG, Groningen, The Netherlands"}]},{"given":"Oscar P.","family":"Kuipers","sequence":"additional","affiliation":[{"name":"1 Molecular Genetics, Groningen Biomolecular Sciences, University of Groningen, PO Box 800, 9700 AV and 2Institute for Mathematics and Computing Science, University of Groningen, Nijenborgh 9, 9747 AG, Groningen, The Netherlands"}]},{"given":"Sacha A. F. T.","family":"van Hijum","sequence":"additional","affiliation":[{"name":"1 Molecular Genetics, Groningen Biomolecular Sciences, University of Groningen, PO Box 800, 9700 AV and 2Institute for Mathematics and Computing Science, University of Groningen, Nijenborgh 9, 9747 AG, Groningen, The Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2009,1,25]]},"reference":[{"key":"2023013110101327500_B1","doi-asserted-by":"crossref","first-page":"1161","DOI":"10.1093\/bioinformatics\/btl658","article-title":"Fiva: Functional information viewer and analyzer extracting biological knowledge from transcriptome data of prokaryotes","volume":"23","author":"Blom","year":"2007","journal-title":"Bioinformatics"},{"key":"2023013110101327500_B2","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1186\/1471-2105-8-249","article-title":"A novel ensemble learning method for de novo computational identification of DNA binding sites","volume":"8","author":"Chakravarty","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023013110101327500_B3","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1016\/j.molcel.2007.09.027","article-title":"A universal framework for regulatory element discovery across all genomes and data types","volume":"28","author":"Elemento","year":"2007","journal-title":"Mol. Cell"},{"key":"2023013110101327500_B4","doi-asserted-by":"crossref","first-page":"3164","DOI":"10.1093\/bioinformatics\/bti481","article-title":"TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs","volume":"21","author":"Gordon","year":"2005","journal-title":"Bioinformatics"},{"key":"2023013110101327500_B5","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1046\/j.1365-2958.2003.03567.x","article-title":"Identification of additional TnrA-regulated genes of Bacillus Subtilis associated with a TnrA box","volume":"49","author":"Yoshida","year":"2003","journal-title":"Mol. Microbiol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/4\/550\/48985300\/bioinformatics_25_4_550.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/4\/550\/48985300\/bioinformatics_25_4_550.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T18:27:33Z","timestamp":1675189653000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/4\/550\/251232"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,1,25]]},"references-count":5,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2009,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp013","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,2,15]]},"published":{"date-parts":[[2009,1,25]]}}}