{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T23:40:52Z","timestamp":1772667652277,"version":"3.50.1"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2016,11,26]],"date-time":"2016-11-26T00:00:00Z","timestamp":1480118400000},"content-version":"vor","delay-in-days":57,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004052","name":"King Abdullah University of Science and Technology","doi-asserted-by":"crossref","award":["URF\/1\/1976-02"],"award-info":[{"award-number":["URF\/1\/1976-02"]}],"id":[{"id":"10.13039\/501100004052","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100004052","name":"King Abdullah University of Science and Technology","doi-asserted-by":"crossref","award":["FCS\/1\/2448-01"],"award-info":[{"award-number":["FCS\/1\/2448-01"]}],"id":[{"id":"10.13039\/501100004052","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The computational search for promoters in prokaryotes remains an attractive problem in bioinformatics. Despite the attention it has received for many years, the problem has not been addressed satisfactorily. In any bacterial genome, the transcription start site is chosen mostly by the sigma (\u03c3) factor proteins, which control the gene activation. The majority of published bacterial promoter prediction tools target \u03c370 promoters in Escherichia coli. Moreover, no \u03c3-specific classification of promoters is available for prokaryotes other than for E. coli.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we introduce bTSSfinder, a novel tool that predicts putative promoters for five classes of \u03c3 factors in Cyanobacteria (\u03c3A, \u03c3C, \u03c3H, \u03c3G and \u03c3F) and for five classes of sigma factors in E. coli (\u03c370, \u03c338, \u03c332, \u03c328 and \u03c324). Comparing to currently available tools, bTSSfinder achieves higher accuracy (MCC\u2009=\u20090.86, F1-score\u2009=\u20090.93) compared to the next best tool with MCC\u2009=\u20090.59, F1-score\u2009=\u20090.79) and covers multiple classes of promoters.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>bTSSfinder is available standalone and online at http:\/\/www.cbrc.kaust.edu.sa\/btssfinder.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw629","type":"journal-article","created":{"date-parts":[[2016,9,29]],"date-time":"2016-09-29T19:06:19Z","timestamp":1475175979000},"page":"334-340","source":"Crossref","is-referenced-by-count":90,"title":["bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and <i>Escherichia coli<\/i>"],"prefix":"10.1093","volume":"33","author":[{"given":"Ilham Ayub","family":"Shahmuradov","sequence":"first","affiliation":[{"name":"Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia"}]},{"given":"Rozaimi","family":"Mohamad Razali","sequence":"additional","affiliation":[{"name":"Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia"}]},{"given":"Salim","family":"Bougouffa","sequence":"additional","affiliation":[{"name":"Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia"}]},{"given":"Aleksandar","family":"Radovanovic","sequence":"additional","affiliation":[{"name":"Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia"}]},{"given":"Vladimir B","family":"Bajic","sequence":"additional","affiliation":[{"name":"Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia"}]}],"member":"286","published-online":{"date-parts":[[2016,9,30]]},"reference":[{"key":"2023020204403406500_btw629-B1","volume-title":"Statistical Analysis: A Computer Oriented Approach","author":"Afifi","year":"2014"},{"key":"2023020204403406500_btw629-B2","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023020204403406500_btw629-B3","doi-asserted-by":"crossref","first-page":"4983","DOI":"10.1128\/JB.00449-12","article-title":"Dual RpoH sigma factors and transcriptional plasticity in a symbiotic bacterium","volume":"194","author":"Barnett","year":"2012","journal-title":"J. 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