{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T13:48:41Z","timestamp":1782308921120,"version":"3.54.5"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T00:00:00Z","timestamp":1781481600000},"content-version":"vor","delay-in-days":14,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Japan Society For The Promotion of Science (JSPS) KAKENHI","award":["JP24H00737"],"award-info":[{"award-number":["JP24H00737"]}]},{"name":"Japan Society For The Promotion of Science (JSPS) KAKENHI","award":["JP22H04925"],"award-info":[{"award-number":["JP22H04925"]}]},{"name":"Japan Society For The Promotion of Science (JSPS) KAKENHI","award":["JP23K28183"],"award-info":[{"award-number":["JP23K28183"]}]},{"name":"Japan Science and Technology Agency (JST) CREST","award":["JPMJCR23N1"],"award-info":[{"award-number":["JPMJCR23N1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>RNA molecules adopt dynamic ensembles of secondary structures, where the local structural context of each nucleotide\u2013such as whether it resides in a stem or a specific type of loop\u2013strongly shapes molecular interactions and regulatory function. Structural-context probabilities therefore provide a more functionally informative view of RNA folding than the minimum free energy structures or base-pairing probabilities. However, existing tools either require O(N3) time or employ span-restricted approximations that omit long-range base-pairs, limiting their applicability to large and biologically important RNAs.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We introduce LinearCapR, enabling linear-time, span-unrestricted computation of structural-context marginalized probabilities, using beam-pruned Stochastic Context Free Grammar-based computation. LinearCapR retains global ensemble features lost by span-limited methods and yields superior predictive power on bpRNA-1m(90) dataset, especially for multiloops and exterior regions, as well as long-distance stems. LinearCapR supports analysis of long RNAs, demonstrated on the full genome of SARS-CoV-2. LinearCapR provides the first base-pair-span-unrestricted, linear-time framework for RNA structural-context analysis, retaining key thermodynamic ensemble features essential for functional interpretation. It enables large-scale studies of viral genomes, long non-coding RNAs, and downstream analyses such as RNA-binding protein site prediction.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and Implementation<\/jats:title>\n                    <jats:p>The source code of LinearCapR is available at https:\/\/github.com\/hoget157\/LinearCapR. The archived software release used in this work is available at Zenodo: https:\/\/doi.org\/10.5281\/zenodo.19450645.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag295","type":"journal-article","created":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T11:44:49Z","timestamp":1781178289000},"source":"Crossref","is-referenced-by-count":0,"title":["LinearCapR: linear-time computation of per-nucleotide structural-context probabilities of RNA without base-pair span limits"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-7123-9585","authenticated-orcid":false,"given":"Takumi","family":"Otagaki","sequence":"first","affiliation":[{"name":"The Department of Computational Biology and Medical Sciences (CBMS), The University of Tokyo , Chiba, 277-8561,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hiroaki","family":"Hosokawa","sequence":"additional","affiliation":[{"name":"The Department of 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