{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,15]],"date-time":"2024-09-15T06:30:59Z","timestamp":1726381859652},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Prediction of transcription factor binding sites (TFBSs) is crucial for promoter modeling and network inference. Quality of the predictions is spoiled by numerous false positives, which persist as the main problem for all presently available TFBS search methods.<\/jats:p>\n               <jats:p>Results: We suggest a novel approach, which is alternative to widely used position weight matrices (PWMs) and Hidden Markov Models. Each motif of the input set is used as a search template to scan a query sequence. Found motifs are assigned scores depending on the non-randomness of the motif's occurrence, the number of matching searching motifs and the number of mismatches. The non-randomness is estimated by comparison of observed numbers of matching motifs with those predicted to occur by chance. The latter can be calculated given the base compositions of the motif and the query sequence. The method does not require preliminary alignment of the input motifs, hence avoiding uncertainties introduced by the alignment procedure. In comparison with PWM-based tools, our method demonstrates higher precision by the same sensitivity and specificity. It also tends to outperform methods combining pattern and PWM search. Most important, it allows reducing the number of false positive predictions significantly.<\/jats:p>\n               <jats:p>Availability: The method is implemented in a tool called SiTaR (Site Tracking and Recognition) and is available at http:\/\/sbi.hki-jena.de\/sitar\/index.php.<\/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\/btr492","type":"journal-article","created":{"date-parts":[[2011,9,6]],"date-time":"2011-09-06T00:26:54Z","timestamp":1315268814000},"page":"2806-2811","source":"Crossref","is-referenced-by-count":11,"title":["SiTaR: a novel tool for transcription factor binding site prediction"],"prefix":"10.1093","volume":"27","author":[{"given":"Eugen","family":"Fazius","sequence":"first","affiliation":[{"name":"Research Group Systems Biology\/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Kn\u00f6ll Institute, 07745 Jena, 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, Hans Kn\u00f6ll Institute, 07745 Jena, 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, Hans Kn\u00f6ll Institute, 07745 Jena, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,9,4]]},"reference":[{"key":"2023012512013327600_B1","first-page":"28","article-title":"Fitting a mixture model by expectation maximization to discover motifs in biopolymers","author":"Bailey","year":"1994","journal-title":"Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology"},{"key":"2023012512013327600_B2","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1007\/978-1-59745-514-5_27","article-title":"Exploring conservation of transcription factor binding sites with CONREAL","volume":"395","author":"Berezikov","year":"2007","journal-title":"Methods Mol. Biol."},{"key":"2023012512013327600_B3","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1016\/0022-2836(87)90354-8","article-title":"Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters","volume":"193","author":"Berg","year":"1987","journal-title":"J. Mol. Biol."},{"key":"2023012512013327600_B4","doi-asserted-by":"crossref","first-page":"D102","DOI":"10.1093\/nar\/gkm955","article-title":"JASPAR, the open access database of transcription factor-bindng profiles: new content and tools in the 2008 update","volume":"36","author":"Bryne","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012512013327600_B5","doi-asserted-by":"crossref","first-page":"2933","DOI":"10.1093\/bioinformatics\/bti473","article-title":"MatInspector and beyond: promoter analysis based on transcription factor binding sites","volume":"21","author":"Cartharius","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012512013327600_B6","doi-asserted-by":"crossref","first-page":"W432","DOI":"10.1093\/nar\/gki441","article-title":"P-Match: transcription factor binding site search by combining patterns and weight matrices","volume":"33","author":"Chekmenev","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012512013327600_B7","doi-asserted-by":"crossref","first-page":"3214","DOI":"10.1093\/nar\/gkf438","article-title":"Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences","volume":"30","author":"Frith","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023012512013327600_B8","doi-asserted-by":"crossref","first-page":"i321","DOI":"10.1093\/bioinformatics\/btp230","article-title":"DISCOVER: a feature-based discriminative method for motif search in complex genomes","volume":"25","author":"Fu","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012512013327600_B9","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1186\/1471-2105-11-551","article-title":"An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs","volume":"11","author":"Garcia-Alcalde","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023012512013327600_B10","first-page":"S1","article-title":"AliBaba2: context specific identification of transcription factor binding sites","volume":"2","author":"Grabe","year":"2002","journal-title":"In Silico Biol."},{"key":"2023012512013327600_B11","doi-asserted-by":"crossref","first-page":"W529","DOI":"10.1093\/nar\/gkl212","article-title":"VOMBAT: prediction of transcription factor binding sites using variable order Bayesian trees","volume":"34","author":"Grau","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012512013327600_B12","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1186\/1471-2105-9-495","article-title":"CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes","volume":"9","author":"Hestand","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023012512013327600_B13","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1046\/j.1365-2958.1999.01667.x","article-title":"Genome-wide analysis of gene expression regulated by the yeast cell wall integrity signalling pathway","volume":"34","author":"Jung","year":"1999","journal-title":"Mol. Microbiol."},{"key":"2023012512013327600_B14","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":"2023012512013327600_B15","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1093\/nar\/gkg108","article-title":"TRANSFAC\u00ae transcriptional regulation, from patterns to profiles","volume":"31","author":"Matys","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012512013327600_B16","doi-asserted-by":"crossref","DOI":"10.2202\/1544-6115.1464","article-title":"Prediction of motifs based on a repeated-measures model for integrating cross-species sequence and expression data","volume":"8","author":"Siewert","year":"2009","journal-title":"Stat. Appl. Genet. Mol. Biol."},{"key":"2023012512013327600_B17","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."},{"key":"2023012512013327600_B18","doi-asserted-by":"crossref","first-page":"1578","DOI":"10.1038\/nprot.2008.97","article-title":"Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules","volume":"3","author":"Turatsinze","year":"2008","journal-title":"Nat. Protoc."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/20\/2806\/48872902\/bioinformatics_27_20_2806.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/20\/2806\/48872902\/bioinformatics_27_20_2806.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T14:09:24Z","timestamp":1674655764000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/20\/2806\/202513"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,9,4]]},"references-count":18,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2011,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr492","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,10,15]]},"published":{"date-parts":[[2011,9,4]]}}}