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Historically, available promoter prediction software have focused on sigma factor-associated promoters in the model organism<jats:italic>E. coli.<\/jats:italic>As a consequence, traditional promoter predictors yield suboptimal predictions when applied to other prokaryotic genera, such as<jats:italic>Pseudomonas,<\/jats:italic>a Gram-negative bacterium of crucial medical and biotechnological importance.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We developed<jats:italic>SAPPHIRE,<\/jats:italic>a promoter predictor for \u03c370 promoters in<jats:italic>Pseudomonas.<\/jats:italic>This promoter prediction relies on an artificial neural network that evaluates sequences on their similarity to the \u2212\u200935 and\u2009\u2212\u200910 boxes of \u03c370 promoters found experimentally in<jats:italic>P. aeruginosa<\/jats:italic>and<jats:italic>P. putida<\/jats:italic>.<jats:italic>SAPPHIRE<\/jats:italic>currently outperforms established predictive software when classifying<jats:italic>Pseudomonas<\/jats:italic>\u03c370 promoters and was built to allow further expansion in the future.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p><jats:italic>SAPPHIRE<\/jats:italic>is the first predictive tool for bacterial \u03c370 promoters in<jats:italic>Pseudomonas<\/jats:italic>. SAPPHIRE is free, publicly available and can be accessed online at<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.biosapphire.com\">www.biosapphire.com<\/jats:ext-link>. Alternatively, users can download the tool as a Python 3 script for local application from this site.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12859-020-03730-z","type":"journal-article","created":{"date-parts":[[2020,10,2]],"date-time":"2020-10-02T15:34:28Z","timestamp":1601652868000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":76,"title":["SAPPHIRE: a neural network based classifier for \u03c370 promoter prediction in Pseudomonas"],"prefix":"10.1186","volume":"21","author":[{"given":"Lucas","family":"Coppens","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7377-1314","authenticated-orcid":false,"given":"Rob","family":"Lavigne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,9,22]]},"reference":[{"key":"3730_CR1","first-page":"28","volume-title":"Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology","author":"T Bailey","year":"1994","unstructured":"Bailey T, Elkan C. 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