{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,26]],"date-time":"2023-01-26T05:20:13Z","timestamp":1674710413958},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The state of the art in promoter modeling for higher eukaryotes is predicting not single transcription factor binding sites (TFBSs), but their combinations. The new tool utilizes a previously developed method of distance distributions of TFBS pairs. We model the random distribution of distances and compare it with the distribution observed in the query sequences. Comparison of the profiles allows filtering out the \u2018noise\u2019 and retaining the potentially functional combinations. This approach has proved its usefulness as a filtering technique for the selection of TFBS pairs for promoter modeling and is now implemented as a tool in R. As an input, it can use the outputs of three different TFBS- and motif-predictive tools (Gibbs Sampler for motifs, MatchTM and MEME\/FIMO for PWM-based search). The output is a list of predicted pairs on overrepresented distances with assigned scores, P-values and plots showing the distribution of pairs in the input sequences.<\/jats:p>\n               <jats:p>Availability: The tool is available at https:\/\/www.omnifung.hki-jena.de\/Rpad\/Distance_Scan\/index.htm<\/jats:p>\n               <jats:p>Contact: \u00a0ekaterina.shelest@hki.jena.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary Data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq132","type":"journal-article","created":{"date-parts":[[2010,3,27]],"date-time":"2010-03-27T00:20:03Z","timestamp":1269649203000},"page":"1460-1462","source":"Crossref","is-referenced-by-count":3,"title":["DistanceScan: a tool for promoter modeling"],"prefix":"10.1093","volume":"26","author":[{"given":"Vladimir","family":"Shelest","sequence":"first","affiliation":[{"name":"Research group Systems Biology\/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Kn\u00f6ll Institute, Beutenbergstr. 11a, 07745 Jena, Germany"}]},{"given":"Daniela","family":"Albrecht","sequence":"additional","affiliation":[{"name":"Research group Systems Biology\/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Kn\u00f6ll Institute, Beutenbergstr. 11a, 07745 Jena, Germany"}]},{"given":"Ekaterina","family":"Shelest","sequence":"additional","affiliation":[{"name":"Research group Systems Biology\/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Kn\u00f6ll Institute, Beutenbergstr. 11a, 07745 Jena, Germany"}]}],"member":"286","published-online":{"date-parts":[[2010,3,25]]},"reference":[{"key":"2023012507502822100_B1","first-page":"28","article-title":"Fitting a mixture model by expectation maximization to discover motifs in biopolymers","volume-title":"Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology.","author":"Bailey","year":"1994"},{"key":"2023012507502822100_B2","first-page":"1","article-title":"Searching for statistically significant regulatory modules","volume":"1","author":"Bailey","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012507502822100_B3","doi-asserted-by":"crossref","first-page":"1202","DOI":"10.1101\/gr.8.11.1202","article-title":"Predicting gene regulatory elements in silico on a genomic scale","volume":"8","author":"Brazma","year":"1998","journal-title":"Genome Res."},{"key":"2023012507502822100_B4","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/S0958-1669(99)00049-X","article-title":"Discovery and modeling of transcriptional regulatory regions","volume":"11","author":"Fickett","year":"2000","journal-title":"Curr. Opin. Biotechnol."},{"key":"2023012507502822100_B5","doi-asserted-by":"crossref","first-page":"3576","DOI":"10.1093\/nar\/gkg585","article-title":"MATCH: a tool for searching transcription factor binding sites in DNA sequences","volume":"31","author":"Kel","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012507502822100_B6","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1093\/nar\/30.1.332","article-title":"TRANSCompel a database on composite regulatory elements in eukaryotic genes","volume":"30","author":"Kel-Margoulis","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023012507502822100_B7","first-page":"193","article-title":"DISTAN - a program which detects significant distances between short oligonucleotides","volume":"3","author":"Konopka","year":"1987","journal-title":"Comput. Appl. 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Bioinformatics analysis and modeling","volume-title":"PhD Thesis","author":"Shelest","year":"2006"},{"key":"2023012507502822100_B10","doi-asserted-by":"crossref","first-page":"3580","DOI":"10.1093\/nar\/gkg608","article-title":"Gibbs Recursive Sampler: finding transcription factor binding sites","volume":"31","author":"Thompson","year":"2003","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/11\/1460\/48850950\/bioinformatics_26_11_1460.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/11\/1460\/48850950\/bioinformatics_26_11_1460.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T07:50:41Z","timestamp":1674633041000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/11\/1460\/202688"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,3,25]]},"references-count":10,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2010,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq132","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,6,1]]},"published":{"date-parts":[[2010,3,25]]}}}