{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T11:08:25Z","timestamp":1760267305218},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"21","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation : Riboswitches are short sequences of messenger RNA that can change their structural conformation to regulate the expression of adjacent genes. Computational prediction of putative riboswitches can provide direction to molecular biologists studying riboswitch-mediated gene expression.<\/jats:p>\n               <jats:p>Results : The Denison Riboswitch Detector (DRD) is a new computational tool with a Web interface that can quickly identify putative riboswitches in DNA sequences on the scale of bacterial genomes. Riboswitch descriptions are easily modifiable and new ones are easily created. The underlying algorithm converts the problem to a \u2018heaviest path\u2019 problem on a multipartite graph, which is then solved using efficient dynamic programming. We show that DRD can achieve \u223c88\u201399% sensitivity and &amp;gt;99.99% specificity on 13 riboswitch families.<\/jats:p>\n               <jats:p>Availability and implementation : DRD is available at http:\/\/drd.denison.edu .<\/jats:p>\n               <jats:p>Contact : havill@denison.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu479","type":"journal-article","created":{"date-parts":[[2014,7,12]],"date-time":"2014-07-12T03:16:15Z","timestamp":1405134975000},"page":"3012-3019","source":"Crossref","is-referenced-by-count":27,"title":["A new approach for detecting riboswitches in DNA sequences"],"prefix":"10.1093","volume":"30","author":[{"given":"Jessen T.","family":"Havill","sequence":"first","affiliation":[{"name":"1 Department of Mathematics and Computer Science, 2 Department of Biology, Denison University, Granville, OH 43023, 3 Capco, New York, NY, 10005, 4 Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109 and 5 College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA"}]},{"given":"Chinmoy","family":"Bhatiya","sequence":"additional","affiliation":[{"name":"1 Department of Mathematics and Computer Science, 2 Department of Biology, Denison University, Granville, OH 43023, 3 Capco, New York, NY, 10005, 4 Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109 and 5 College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA"}]},{"given":"Steven M.","family":"Johnson","sequence":"additional","affiliation":[{"name":"1 Department of Mathematics and Computer Science, 2 Department of Biology, Denison University, Granville, OH 43023, 3 Capco, New York, NY, 10005, 4 Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109 and 5 College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA"}]},{"given":"Joseph D.","family":"Sheets","sequence":"additional","affiliation":[{"name":"1 Department of Mathematics and Computer Science, 2 Department of Biology, Denison University, Granville, OH 43023, 3 Capco, New York, NY, 10005, 4 Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109 and 5 College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA"}]},{"given":"Jeffrey S.","family":"Thompson","sequence":"additional","affiliation":[{"name":"1 Department of Mathematics and Computer Science, 2 Department of Biology, Denison University, Granville, OH 43023, 3 Capco, New York, NY, 10005, 4 Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109 and 5 College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA"}]}],"member":"286","published-online":{"date-parts":[[2014,7,11]]},"reference":[{"key":"2023012711574740500_btu479-B1","doi-asserted-by":"crossref","first-page":"W690","DOI":"10.1093\/nar\/gki445","article-title":"RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements","volume":"33","author":"Abreu-Goodger","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012711574740500_btu479-B2","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1017\/S0033583512000078","article-title":"Structure and mechanism of purine-binding riboswitches","volume":"45","author":"Batey","year":"2012","journal-title":"Q. 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