{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T14:57:35Z","timestamp":1776092255571,"version":"3.50.1"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation:\u2003Traditional and high-throughput techniques for determining transcription factor (TF) binding specificities are generating large volumes of data of uneven quality, which are scattered across individual databases.<\/jats:p>\n               <jats:p>Results:\u2003FootprintDB integrates some of the most comprehensive freely available libraries of curated DNA binding sites and systematically annotates the binding interfaces of the corresponding TFs. The first release contains 2422 unique TF sequences, 10 112 DNA binding sites and 3662 DNA motifs. A survey of the included data sources, organisms and TF families was performed together with proprietary database TRANSFAC, finding that footprintDB has a similar coverage of multicellular organisms, while also containing bacterial regulatory data. A search engine has been designed that drives the prediction of DNA motifs for input TFs, or conversely of TF sequences that might recognize input regulatory sequences, by comparison with database entries. Such predictions can also be extended to a single proteome chosen by the user, and results are ranked in terms of interface similarity. Benchmark experiments with bacterial, plant and human data were performed to measure the predictive power of footprintDB searches, which were able to correctly recover 10, 55 and 90% of the tested sequences, respectively. Correctly predicted TFs had a higher interface similarity than the average, confirming its diagnostic value.<\/jats:p>\n               <jats:p>Availability and implementation:\u2003Web site implemented in PHP, Perl, MySQL and Apache. Freely available from http:\/\/floresta.eead.csic.es\/footprintdb.<\/jats:p>\n               <jats:p>Contact:\u2002bioquimicas@yahoo.es; bcontreras@eead.csic.es<\/jats:p>\n               <jats:p>Supplementary information:\u2003Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt663","type":"journal-article","created":{"date-parts":[[2013,11,15]],"date-time":"2013-11-15T01:30:49Z","timestamp":1384479049000},"page":"258-265","source":"Crossref","is-referenced-by-count":81,"title":["footprintDB: a database of transcription factors with annotated cis elements and binding interfaces"],"prefix":"10.1093","volume":"30","author":[{"given":"Alvaro","family":"Sebastian","sequence":"first","affiliation":[{"name":"1 Laboratory of Computational Biology, Department of Genetics and Plant Production, Estaci\u00f3n Experimental de Aula Dei\/CSIC, Av. Monta\u00f1ana 1005, Zaragoza (http:\/\/www.eead.csic.es\/compbio) and 2Fundaci\u00f3n ARAID, Paseo Mar\u00eda Agust\u00edn 36, Zaragoza, Spain"}]},{"given":"Bruno","family":"Contreras-Moreira","sequence":"additional","affiliation":[{"name":"1 Laboratory of Computational Biology, Department of Genetics and Plant Production, Estaci\u00f3n Experimental de Aula Dei\/CSIC, Av. Monta\u00f1ana 1005, Zaragoza (http:\/\/www.eead.csic.es\/compbio) and 2Fundaci\u00f3n ARAID, Paseo Mar\u00eda Agust\u00edn 36, Zaragoza, Spain"},{"name":"1 Laboratory of Computational Biology, Department of Genetics and Plant Production, Estaci\u00f3n Experimental de Aula Dei\/CSIC, Av. Monta\u00f1ana 1005, Zaragoza (http:\/\/www.eead.csic.es\/compbio) and 2Fundaci\u00f3n ARAID, Paseo Mar\u00eda Agust\u00edn 36, Zaragoza, Spain"}]}],"member":"286","published-online":{"date-parts":[[2013,11,14]]},"reference":[{"key":"2023012710392004900_btt663-B1","doi-asserted-by":"crossref","first-page":"14819","DOI":"10.1073\/pnas.1106460108","article-title":"Direct inference of protein-DNA interactions using compressed sensing methods","volume":"108","author":"AlQuraishi","year":"2011","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012710392004900_btt663-B2","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. 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