{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,7]],"date-time":"2026-01-07T22:46:49Z","timestamp":1767826009794,"version":"3.49.0"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":458,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Gene transcription is mostly conducted through interactions of various transcription factors and their binding sites on DNA (regulatory elements, REs). Today, we are still far from understanding the real regulatory content of promoter regions. Computer methods for identification of REs remain a widely used tool for studying and understanding transcriptional regulation mechanisms. The Nsite, NsiteH and NsiteM programs perform searches for statistically significant (non-random) motifs of known human, animal and plant one-box and composite REs in a single genomic sequence, in a pair of aligned homologous sequences and in a set of functionally related sequences, respectively.<\/jats:p>\n               <jats:p>Availability and implementation: Pre-compiled executables built under commonly used operating systems are available for download by visiting http:\/\/www.molquest.kaust.edu.sa and http:\/\/www.softberry.com.<\/jats:p>\n               <jats:p>Contact: \u00a0solovictor@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv404","type":"journal-article","created":{"date-parts":[[2015,7,4]],"date-time":"2015-07-04T00:09:25Z","timestamp":1435968565000},"page":"3544-3545","source":"Crossref","is-referenced-by-count":54,"title":["Nsite, NsiteH and NsiteM computer tools for studying transcription regulatory elements"],"prefix":"10.1093","volume":"31","author":[{"given":"Ilham A.","family":"Shahmuradov","sequence":"first","affiliation":[{"name":"1 Computer, Electrical and Mathematical Sciences and Engineering Division, KAUST, Thuwal 23955-6900, KSA,"},{"name":"2 Bioinformatics laboratory, Institute of Botany, ANAS, Baku AZ1073, Azerbaijan and"}]},{"given":"Victor V.","family":"Solovyev","sequence":"additional","affiliation":[{"name":"1 Computer, Electrical and Mathematical Sciences and Engineering Division, KAUST, Thuwal 23955-6900, KSA,"},{"name":"3 Bioinformatics Division, Softberry Inc., Mount Kisco, NY 10549, USA"}]}],"member":"286","published-online":{"date-parts":[[2015,7,2]]},"reference":[{"key":"2023020202344315900_btv404-B1","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.plantsci.2012.05.005","article-title":"The regulation of the SARK promoter activity by hormones and environmental signals","volume":"193\u2013194","author":"Delatorre","year":"2012","journal-title":"Plant Sci."},{"key":"2023020202344315900_btv404-B2","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1093\/nar\/28.1.308","article-title":"Object-oriented Transcription Factors Database (ooTFD)","volume":"28","author":"Ghosh","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023020202344315900_btv404-B3","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1016\/j.tibs.2013.09.002","article-title":"Structural insights into transcription by RNA polymerase II","volume":"38","author":"Gr\u00fcnberg","year":"2013","journal-title":"Trends Biochem. 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