{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T12:43:46Z","timestamp":1773665026982,"version":"3.50.1"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Footprint data is an important source of information on transcription factor recognition motifs. However, a footprinting fragment can contain no sequences similar to known protein recognition sites. Inspection of genome fragments nearby can help to identify missing site positions.<\/jats:p>\n               <jats:p>Results: Genome fragments containing footprints were supplied to a pipeline that constructed a position weight matrix (PWM) for different motif lengths and selected the optimal PWM. Fragments were aligned with the SeSiMCMC sampler and a new heuristic algorithm, Bigfoot. Footprints with missing hits were found for \u223c50% of factors. Adding only 2 bp on both sides of a footprinting fragment recovered most hits. We automatically constructed motifs for 41 Drosophila factors. New motifs can recognize footprints with a greater sensitivity at the same false positive rate than existing models. Also we discuss possible overfitting of constructed motifs.<\/jats:p>\n               <jats:p>Availability: Software and the collection of regulatory motifs are freely available at http:\/\/line.imb.ac.ru\/DMMPMM.<\/jats:p>\n               <jats:p>Contact: \u00a0ivan.kulakovskiy@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0http:\/\/line.imb.ac.ru\/DMMPMM<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp434","type":"journal-article","created":{"date-parts":[[2009,7,16]],"date-time":"2009-07-16T00:49:46Z","timestamp":1247705386000},"page":"2318-2325","source":"Crossref","is-referenced-by-count":34,"title":["Motif discovery and motif finding from genome-mapped DNase footprint data"],"prefix":"10.1093","volume":"25","author":[{"given":"Ivan V.","family":"Kulakovskiy","sequence":"first","affiliation":[{"name":"1 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow 119991, 2State Scientific Institute of Genetics and Selection of Industrial Microorganisms, GosNIIgenetika, 1st Dorozhny proezd, 1, Moscow 117545, Russia and 3The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA"},{"name":"1 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow 119991, 2State Scientific Institute of Genetics and Selection of Industrial Microorganisms, GosNIIgenetika, 1st Dorozhny proezd, 1, Moscow 117545, Russia and 3The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA"}]},{"given":"Alexander V.","family":"Favorov","sequence":"additional","affiliation":[{"name":"1 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow 119991, 2State Scientific Institute of Genetics and Selection of Industrial Microorganisms, GosNIIgenetika, 1st Dorozhny proezd, 1, Moscow 117545, Russia and 3The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA"},{"name":"1 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow 119991, 2State Scientific Institute of Genetics and Selection of Industrial Microorganisms, GosNIIgenetika, 1st Dorozhny proezd, 1, Moscow 117545, Russia and 3The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA"}]},{"given":"Vsevolod J.","family":"Makeev","sequence":"additional","affiliation":[{"name":"1 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow 119991, 2State Scientific Institute of Genetics and Selection of Industrial Microorganisms, GosNIIgenetika, 1st Dorozhny proezd, 1, Moscow 117545, Russia and 3The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA"},{"name":"1 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow 119991, 2State Scientific Institute of Genetics and Selection of Industrial Microorganisms, GosNIIgenetika, 1st Dorozhny proezd, 1, Moscow 117545, Russia and 3The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,7,15]]},"reference":[{"key":"2023013112122151300_B1","volume-title":"Handbook of Mathematical Functions.","author":"Abramowitz","year":"1972"},{"key":"2023013112122151300_B2","first-page":"2.4.1","article-title":"Discovering Novel Sequence Motifs with MEME","volume-title":"Current Protocols in Bioinformatics","author":"Bailey","year":"2002"},{"key":"2023013112122151300_B3","doi-asserted-by":"crossref","first-page":"1747","DOI":"10.1093\/bioinformatics\/bti173","article-title":"Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster","volume":"21","author":"Bergman","year":"2005","journal-title":"Bioinformatics"},{"key":"2023013112122151300_B4","doi-asserted-by":"crossref","first-page":"1104","DOI":"10.1126\/science.2174572","article-title":"Differences and similarities in DNA-binding preferences of MyoD and E2A protein complexes revealed by binding site selection","volume":"250","author":"Blackwell","year":"1990","journal-title":"Science"},{"key":"2023013112122151300_B5","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1089\/10665270252935421","article-title":"Algorithms for phylogenetic footprinting","volume":"9","author":"Blanchette","year":"2002","journal-title":"J. Comput. Biol."},{"key":"2023013112122151300_B6","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1093\/bioinformatics\/btk032","article-title":"Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression","volume":"22","author":"Boeva","year":"2006","journal-title":"Bioinformatics"},{"key":"2023013112122151300_B7","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/1748-7188-2-13","article-title":"Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules","volume":"2","author":"Boeva","year":"2007","journal-title":"Algorithms Mol. 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