{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,20]],"date-time":"2026-02-20T14:15:24Z","timestamp":1771596924077,"version":"3.50.1"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"Supplement_1","license":[{"start":{"date-parts":[[2024,6,28]],"date-time":"2024-06-28T00:00:00Z","timestamp":1719532800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","award":["499552394"],"award-info":[{"award-number":["499552394"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","award":["417962828"],"award-info":[{"award-number":["417962828"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","award":["INST 39\/963-1"],"award-info":[{"award-number":["INST 39\/963-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000780","name":"European Union","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"name":"ERC Consolidator Grant DeepLearning 2.0","award":["101045765"],"award-info":[{"award-number":["101045765"]}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000780","name":"European Union","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,6,28]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>RNA design is a key technique to achieve new functionality in fields like synthetic biology or biotechnology. Computational tools could help to find such RNA sequences but they are often limited in their formulation of the search space.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>In this work, we propose partial RNA design, a novel RNA design paradigm that addresses the limitations of current RNA design formulations. Partial RNA design describes the problem of designing RNAs from arbitrary RNA sequences and structure motifs with multiple design goals. By separating the design space from the objectives, our formulation enables the design of RNAs with variable lengths and desired properties, while still allowing precise control over sequence and structure constraints at individual positions. Based on this formulation, we introduce a new algorithm, libLEARNA, capable of efficiently solving different constraint RNA design tasks. A comprehensive analysis of various problems, including a realistic riboswitch design task, reveals the outstanding performance of libLEARNA and its robustness.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and Implementation<\/jats:title><jats:p>libLEARNA is open-source and publicly available at: https:\/\/github.com\/automl\/learna_tools.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae222","type":"journal-article","created":{"date-parts":[[2024,6,28]],"date-time":"2024-06-28T09:33:06Z","timestamp":1719567186000},"page":"i437-i445","source":"Crossref","is-referenced-by-count":12,"title":["Partial RNA design"],"prefix":"10.1093","volume":"40","author":[{"given":"Frederic","family":"Runge","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of Freiburg , Freiburg 79110, Germany"}]},{"given":"J\u00f6rg","family":"Franke","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Freiburg , Freiburg 79110, Germany"}]},{"given":"Daniel","family":"Fertmann","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Freiburg , Freiburg 79110, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8231-3323","authenticated-orcid":false,"given":"Rolf","family":"Backofen","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Freiburg , Freiburg 79110, Germany"}]},{"given":"Frank","family":"Hutter","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Freiburg , Freiburg 79110, Germany"}]}],"member":"286","published-online":{"date-parts":[[2024,6,28]]},"reference":[{"key":"2024071814121265200_btae222-B1","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1016\/j.jmb.2003.12.041","article-title":"A new algorithm for RNA secondary structure design","volume":"336","author":"Andronescu","year":"2004","journal-title":"J Mol 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