{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T04:14:07Z","timestamp":1771474447864,"version":"3.50.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary : Supercoiling imposes stress on a DNA molecule that can drive susceptible sequences into alternative non-B form structures. This phenomenon occurs frequently in vivo and has been implicated in biological processes, such as replication, transcription, recombination and translocation. SIST is a software package that analyzes sequence-dependent structural transitions in kilobase length superhelical DNA molecules. The numerical algorithms in SIST are based on a statistical mechanical model that calculates the equilibrium probability of transition for each base pair in the domain. They are extensions of the original stress-induced duplex destabilization (SIDD) method, which analyzes stress-driven DNA strand separation. SIST also includes algorithms to analyze B-Z transitions and cruciform extrusion. The SIST pipeline has an option to use the DZCB trans algorithm, which analyzes the competition among these three transitions within a superhelical domain.<\/jats:p>\n               <jats:p>Availability and implementation : The package and additional documentation are freely available at https:\/\/bitbucket.org\/benhamlab\/sist_codes .<\/jats:p>\n               <jats:p>Contact : dzhabinskaya@ucdavis.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu657","type":"journal-article","created":{"date-parts":[[2014,10,5]],"date-time":"2014-10-05T00:35:52Z","timestamp":1412469352000},"page":"421-422","source":"Crossref","is-referenced-by-count":30,"title":["SIST: stress-induced structural transitions in superhelical DNA"],"prefix":"10.1093","volume":"31","author":[{"given":"Dina","family":"Zhabinskaya","sequence":"first","affiliation":[{"name":"1 UC Davis Genome Center and 2 Department of Mathematics, University of California, Davis, CA 95616, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sally","family":"Madden","sequence":"additional","affiliation":[{"name":"1 UC Davis Genome Center and 2 Department of Mathematics, University of California, Davis, CA 95616, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Craig J.","family":"Benham","sequence":"additional","affiliation":[{"name":"1 UC Davis Genome Center and 2 Department of Mathematics, University of California, Davis, CA 95616, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,10,4]]},"reference":[{"key":"2023020116164007400_btu657-B1","doi-asserted-by":"crossref","first-page":"3408","DOI":"10.1103\/PhysRevE.59.3408","article-title":"Exact method for numerically analyzing a model of local denaturation in superhelically stressed DNA","volume":"59","author":"Fye","year":"1999","journal-title":"Phys. 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Biol."},{"key":"2023020116164007400_btu657-B5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pcbi.1002484","article-title":"Theoretical analysis of competing conformational transitions in superhelical dna","volume":"8","author":"Zhabinskaya","year":"2012","journal-title":"PLoS Comput. Biol."},{"key":"2023020116164007400_btu657-B6","doi-asserted-by":"crossref","first-page":"9610","DOI":"10.1093\/nar\/gkt733","article-title":"Competitive superhelical transitions involving cruciform extrusion","volume":"41","author":"Zhabinskaya","year":"2013","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/3\/421\/49013153\/bioinformatics_31_3_421.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/3\/421\/49013153\/bioinformatics_31_3_421.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T00:17:27Z","timestamp":1675297047000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/3\/421\/2365978"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,10,4]]},"references-count":6,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2015,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu657","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,2,1]]},"published":{"date-parts":[[2014,10,4]]}}}