{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:14:31Z","timestamp":1787008471431,"version":"build-2736575974"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Background: A small class of RNA molecules, in particular the tiny genomes of viroids, are circular. Yet most structure prediction algorithms handle only linear RNAs. The most straightforward approach is to compute circular structures from \u2018internal\u2019 and \u2018external\u2019 substructures separated by a base pair. This is incompatible, however, with the memory-saving approach of the Vienna RNA Package which builds a linear RNA structure from shorter (internal) structures only.<\/jats:p>\n                  <jats:p>Result: Here we describe how circular secondary structures can be obtained without additional memory requirements as a kind of \u2018post-processing\u2019 of the linear structures.<\/jats:p>\n                  <jats:p>Availability: The circular folding algorithm is implemented in the current version of the of RNAfold program of the Vienna RNA Package, which can be downloaded from<\/jats:p>\n                  <jats:p>Contact: \u00a0ivo@tbi.univie.ac.at<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl023","type":"journal-article","created":{"date-parts":[[2006,2,1]],"date-time":"2006-02-01T20:24:44Z","timestamp":1138825484000},"page":"1172-1176","source":"Crossref","is-referenced-by-count":179,"title":["Memory efficient folding algorithms for circular RNA secondary structures"],"prefix":"10.1093","volume":"22","author":[{"given":"Ivo L.","family":"Hofacker","sequence":"first","affiliation":[{"name":"Institute for Theoretical Chemistry, University of Vienna 1 \u00a0 1 \u00a0 \u00a0 W\u00e4hringerstr. 17, A-1090 Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter F.","family":"Stadler","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig 2 \u00a0 2 \u00a0 \u00a0 H\u00e4rtelstrasse 16-18, D-04107 Leipzig, Germany"},{"name":"Institute for Theoretical Chemistry, University of Vienna 1 \u00a0 1 \u00a0 \u00a0 W\u00e4hringerstr. 17, A-1090 Vienna, Austria"},{"name":"The Santa Fe Institute 3 \u00a0 3 \u00a0 \u00a0 1399 Hyde Park Road, Santa Fe, NM, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2006,2,1]]},"reference":[{"key":"2023012408205957300_b1","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1016\/j.febslet.2004.03.118","article-title":"Viroids: the minimal non-coding RNAs with autonomous replication","volume":"567","author":"Flores","year":"2004","journal-title":"FEBS Lett."},{"key":"2023012408205957300_b2","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1109\/34.192484","article-title":"Dynamic programming alignment of sequences representing cyclic patterns","volume":"15","author":"Gregor","year":"1993","journal-title":"IEEE Trans. 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