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Because it is infeasible to construct an efficiently computable secondary structure model including pseudoknots, secondary structure prediction methods considering pseudoknots are not yet widely available. We developed IPknot, which uses heuristics to speed up computations, but it has remained difficult to apply it to long sequences, such as messenger RNA and viral RNA, because it requires cubic computational time with respect to sequence length and has threshold parameters that need to be manually adjusted. Here, we propose an improvement of IPknot that enables calculation in linear time by employing the LinearPartition model and automatically selects the optimal threshold parameters based on the pseudo-expected accuracy. In addition, IPknot showed favorable prediction accuracy across a wide range of conditions in our exhaustive benchmarking, not only for single sequences but also for multiple alignments.<\/jats:p>","DOI":"10.1093\/bib\/bbab395","type":"journal-article","created":{"date-parts":[[2021,9,8]],"date-time":"2021-09-08T11:20:51Z","timestamp":1631100051000},"source":"Crossref","is-referenced-by-count":65,"title":["Prediction of RNA secondary structure including pseudoknots for long sequences"],"prefix":"10.1093","volume":"23","author":[{"given":"Kengo","family":"Sato","sequence":"first","affiliation":[{"name":"Department of Biosciences and Informatics, Keio University, 3\u201314\u20131 Hiyoshi, Kohoku-ku, Yokohama 223\u20138522, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuki","family":"Kato","sequence":"additional","affiliation":[{"name":"Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565\u20130871, Japan"},{"name":"Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565\u20130871, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,10,2]]},"reference":[{"issue":"13","key":"2022011921121945900_ref1","doi-asserted-by":"crossref","first-page":"3406","DOI":"10.1093\/nar\/gkg595","article-title":"Mfold web server for nucleic acid folding and hybridization prediction","volume":"31","author":"Zuker","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2022011921121945900_ref2","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1186\/1748-7188-6-26","article-title":"ViennaRNA package 2.0","volume":"6","author":"Lorenz","year":"2011","journal-title":"Algorithms Mol 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