{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T12:43:56Z","timestamp":1781613836144,"version":"3.54.5"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Many computational methods for RNA secondary structure prediction, and, in particular, for the prediction of a consensus structure of an alignment of RNA sequences, have been developed. Most methods, however, ignore biophysical factors, such as the kinetics of RNA folding; no current implementation considers both evolutionary information and folding kinetics, thus losing information that, when considered, might lead to better predictions.<\/jats:p>\n               <jats:p>Results: We present an iterative algorithm, Oxfold, in the framework of stochastic context-free grammars, that emulates the kinetics of RNA folding in a simplified way, in combination with a molecular evolution model. This method improves considerably on existing grammatical models that do not consider folding kinetics. Additionally, the model compares favourably to non-kinetic thermodynamic models.<\/jats:p>\n               <jats:p>Availability: http:\/\/www.stats.ox.ac.uk\/\u223canderson.<\/jats:p>\n               <jats:p>Contact: anderson@stats.ox.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt050","type":"journal-article","created":{"date-parts":[[2013,2,10]],"date-time":"2013-02-10T01:09:00Z","timestamp":1360458540000},"page":"704-710","source":"Crossref","is-referenced-by-count":12,"title":["Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information"],"prefix":"10.1093","volume":"29","author":[{"given":"James W. J.","family":"Anderson","sequence":"first","affiliation":[{"name":"1 Department of Statistics, Oxford University, 1 South Parks Road, Oxford OX1 3TG, UK, 2Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK, 3Department of Computer Science, University of British Columbia, 201-2366 Main Mall, Vancouver, B.C., V6T 1Z4, Canada, 4European Bioinformatics Institute, Hinxton, Cambridgeshire CB10 1SD, UK and 5Bioinformatics Research Centre, Aarhus University, C.F. M\u00f8llers All\u00e9 8, DK-8000 Aarhus C, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pierre A.","family":"Haas","sequence":"additional","affiliation":[{"name":"1 Department of Statistics, Oxford University, 1 South Parks Road, Oxford OX1 3TG, UK, 2Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK, 3Department of Computer Science, University of British Columbia, 201-2366 Main Mall, Vancouver, B.C., V6T 1Z4, Canada, 4European Bioinformatics Institute, Hinxton, Cambridgeshire CB10 1SD, UK and 5Bioinformatics Research Centre, Aarhus University, C.F. M\u00f8llers All\u00e9 8, DK-8000 Aarhus C, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leigh-Anne","family":"Mathieson","sequence":"additional","affiliation":[{"name":"1 Department of Statistics, Oxford University, 1 South Parks Road, Oxford OX1 3TG, UK, 2Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK, 3Department of Computer Science, University of British Columbia, 201-2366 Main Mall, Vancouver, B.C., V6T 1Z4, Canada, 4European Bioinformatics Institute, Hinxton, Cambridgeshire CB10 1SD, UK and 5Bioinformatics Research Centre, Aarhus University, C.F. M\u00f8llers All\u00e9 8, DK-8000 Aarhus C, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vladimir","family":"Volynkin","sequence":"additional","affiliation":[{"name":"1 Department of Statistics, Oxford University, 1 South Parks Road, Oxford OX1 3TG, UK, 2Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK, 3Department of Computer Science, University of British Columbia, 201-2366 Main Mall, Vancouver, B.C., V6T 1Z4, Canada, 4European Bioinformatics Institute, Hinxton, Cambridgeshire CB10 1SD, UK and 5Bioinformatics Research Centre, Aarhus University, C.F. 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