{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,22]],"date-time":"2026-06-22T11:19:40Z","timestamp":1782127180832,"version":"3.54.5"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2023,1,19]],"date-time":"2023-01-19T00:00:00Z","timestamp":1674086400000},"content-version":"vor","delay-in-days":18,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Austrian Science Foundation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Folding during transcription can have an important influence on the structure and function of RNA molecules, as regions closer to the 5\u2032 end can fold into metastable structures before potentially stronger interactions with the 3\u2032 end become available. Thermodynamic RNA folding models are not suitable to predict structures that result from cotranscriptional folding, as they can only calculate properties of the equilibrium distribution. Other software packages that simulate the kinetic process of RNA folding during transcription exist, but they are mostly applicable for short sequences.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present a new algorithm that tracks changes to the RNA secondary structure ensemble during transcription. At every transcription step, new representative local minima are identified, a neighborhood relation is defined and transition rates are estimated for kinetic simulations. After every simulation, a part of the ensemble is removed and the remainder is used to search for new representative structures. The presented algorithm is deterministic (up to numeric instabilities of simulations), fast (in comparison with existing methods), and it is capable of folding RNAs much longer than 200 nucleotides.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>This software is open-source and available at https:\/\/github.com\/ViennaRNA\/drtransformer.<\/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\/btad034","type":"journal-article","created":{"date-parts":[[2023,1,18]],"date-time":"2023-01-18T07:32:52Z","timestamp":1674027172000},"source":"Crossref","is-referenced-by-count":11,"title":["<tt>DrTransformer<\/tt>\n                    : heuristic cotranscriptional RNA folding using the nearest neighbor energy model"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2636-5801","authenticated-orcid":false,"given":"Stefan","family":"Badelt","sequence":"first","affiliation":[{"name":"Department of Theoretical Chemistry, University of Vienna , Vienna, Austria"},{"name":"Division of Biology and Biological Engineering, California Institute of Technology , Pasadena, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2144-698X","authenticated-orcid":false,"given":"Ronny","family":"Lorenz","sequence":"additional","affiliation":[{"name":"Department of Theoretical Chemistry, University of Vienna , Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7132-0800","authenticated-orcid":false,"given":"Ivo L","family":"Hofacker","sequence":"additional","affiliation":[{"name":"Department of Theoretical Chemistry, University of Vienna , Vienna, Austria"},{"name":"Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna , Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,1,19]]},"reference":[{"key":"2023020106544472800_btad034-B1","first-page":"193","author":"Badelt","year":"2015"},{"key":"2023020106544472800_btad034-B2","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1142\/S0219720006001904","article-title":"RNAKinetics: a web server that models secondary structure kinetics of an elongating RNA","volume":"4","author":"Danilova","year":"2006","journal-title":"J. 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