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Despite their central role, deciphering shape recognition of bacterial TFs-DNA interactions remains an intricate challenge. A deeper understanding of DNA secondary structures could greatly enhance our knowledge of how TFs recognize and interact with DNA, thereby elucidating their biological function. In this study, we employed machine learning algorithms to predict transcription factor binding sites (TFBS) and classify them as directed-repeat (DR) or inverted-repeat (IR). To accomplish this, we divided the set of TFBS nucleotide sequences by size, ranging from 8 to 20 base pairs, and converted them into thermodynamic data known as DNA duplex stability (DDS). Our results demonstrate that the Random Forest algorithm accurately predicts TFBS with an average accuracy of over 82% and effectively distinguishes between IR and DR with an accuracy of 89%. Interestingly, upon converting the base pairs of several TFBS-IR into DDS values, we observed a symmetric profile typical of the palindromic structure associated with these architectures. This study presents a novel TFBS prediction model based on a DDS characteristic that may indicate how respective proteins interact with base pairs, thus providing insights into molecular mechanisms underlying bacterial TFs-DNA interaction.<\/jats:p>","DOI":"10.1093\/bib\/bbae581","type":"journal-article","created":{"date-parts":[[2024,11,14]],"date-time":"2024-11-14T16:07:02Z","timestamp":1731600422000},"source":"Crossref","is-referenced-by-count":5,"title":["Predicting bacterial transcription factor binding sites through machine learning and structural characterization based on DNA duplex stability"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4699-0199","authenticated-orcid":false,"given":"Andr\u00e9","family":"Borges Farias","sequence":"first","affiliation":[{"name":"Laborat\u00f3rio Nacional de Computa\u00e7\u00e3o Cient\u00edfica - LNCC , Avenida Get\u00falio Vargas, Petr\u00f3polis, Rio de Janeiro 25651075 ,","place":["Brazil"]},{"name":"Instituto de Investigaciones en Matem\u00e1ticas Aplicadas y en Sistemas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Unidad Acad\u00e9mica del Estado de Yucat\u00e1n , Carretera Sierra Papacal, M\u00e9rida 97302, Yucat\u00e1n ,","place":["M\u00e9xico"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7656-0579","authenticated-orcid":false,"given":"Gustavo","family":"Sganzerla Martinez","sequence":"additional","affiliation":[{"name":"Microbiology and Immunology, Dalhousie University , 5850 College Street, Halifax B3H 4H7, Nova Scotia ,","place":["Canada"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9165-1241","authenticated-orcid":false,"given":"Edgardo","family":"Gal\u00e1n-V\u00e1squez","sequence":"additional","affiliation":[{"name":"Departamento de Ingenier\u00eda de Sistemas Computacionales y Automatizaci\u00f3n , Instituto de Investigaciones en Matem\u00e1ticas Aplicadas y en Sistemas, , Circuito Escolar S\/N, Mexico City 01000 ,","place":["M\u00e9xico"]},{"name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico, Ciudad Universitaria , Instituto de Investigaciones en Matem\u00e1ticas Aplicadas y en Sistemas, , Circuito Escolar S\/N, Mexico City 01000 ,","place":["M\u00e9xico"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5437-2737","authenticated-orcid":false,"given":"Marisa Fabiana","family":"Nicol\u00e1s","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio Nacional de Computa\u00e7\u00e3o Cient\u00edfica - LNCC , Avenida Get\u00falio Vargas, Petr\u00f3polis, Rio de Janeiro 25651075 ,","place":["Brazil"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6879-0673","authenticated-orcid":false,"given":"Ernesto","family":"P\u00e9rez-Rueda","sequence":"additional","affiliation":[{"name":"Instituto de Investigaciones en Matem\u00e1ticas Aplicadas y en Sistemas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Unidad Acad\u00e9mica del Estado de Yucat\u00e1n , Carretera Sierra Papacal, M\u00e9rida 97302, 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