{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T11:31:39Z","timestamp":1740137499174,"version":"3.37.3"},"reference-count":11,"publisher":"World Scientific Pub Co Pte Ltd","issue":"03","funder":[{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea (KR)","doi-asserted-by":"publisher","award":["2015R1A1A3A04001243"],"award-info":[{"award-number":["2015R1A1A3A04001243"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002701","name":"Ministry of Education (KR)","doi-asserted-by":"publisher","award":["2010-0020163"],"award-info":[{"award-number":["2010-0020163"]}],"id":[{"id":"10.13039\/501100002701","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2016,6]]},"abstract":"<jats:p> An RNA pseudoknot is a tertiary structural element in which bases of a loop pair with complementary bases are outside the loop. A drawing of RNA secondary structures is a tree, but a drawing of RNA pseudoknots is a graph that has an inner cycle within a pseudoknot and possibly outer cycles formed between the pseudoknot and other structural elements. Visualizing a large-scale RNA structure with pseudoknots as a planar drawing is challenging because a planar drawing of an RNA structure requires both pseudoknots and an entire structure enclosing the pseudoknots to be embedded into a plane without overlapping or crossing. This paper presents an efficient heuristic algorithm for visualizing a pseudoknotted RNA structure as a planar drawing. The algorithm consists of several parts for finding crossing stems and page mapping the stems, for the layout of stem-loops and pseudoknots, and for overlap detection between structural elements and resolving it. Unlike previous algorithms, our algorithm generates a planar drawing for a large RNA structure with pseudoknots of any type and provides a bracket view of the structure. It generates a compact and aesthetic structure graph for a large pseudoknotted RNA structure in O([Formula: see text]) time, where n is the number of stems of the RNA structure. <\/jats:p>","DOI":"10.1142\/s0219720016500098","type":"journal-article","created":{"date-parts":[[2016,3,2]],"date-time":"2016-03-02T06:02:37Z","timestamp":1456898557000},"page":"1650009","source":"Crossref","is-referenced-by-count":1,"title":["An efficient algorithm for planar drawing of RNA structures with pseudoknots of any type"],"prefix":"10.1142","volume":"14","author":[{"given":"Yanga","family":"Byun","sequence":"first","affiliation":[{"name":"Department of Computer Science and Engineering, Inha University, Incheon 402-751, Korea"}]},{"given":"Kyungsook","family":"Han","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, Inha University, Incheon 402-751, Korea"}]}],"member":"219","published-online":{"date-parts":[[2016,6,14]]},"reference":[{"key":"S0219720016500098BIB001","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/18.suppl_1.S321"},{"key":"S0219720016500098BIB002","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/19.2.299"},{"key":"S0219720016500098BIB003","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/15.1.32"},{"key":"S0219720016500098BIB004","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg599"},{"key":"S0219720016500098BIB006","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg539"},{"key":"S0219720016500098BIB007","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/29.1.194"},{"key":"S0219720016500098BIB008","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp252"},{"key":"S0219720016500098BIB009","doi-asserted-by":"publisher","DOI":"10.1006\/bulm.1998.0085"},{"key":"S0219720016500098BIB010","doi-asserted-by":"publisher","DOI":"10.1016\/0095-8956(79)90021-2"},{"key":"S0219720016500098BIB011","doi-asserted-by":"publisher","DOI":"10.1533\/9780857099686"},{"key":"S0219720016500098BIB012","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-3-2"}],"container-title":["Journal of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.worldscientific.com\/doi\/pdf\/10.1142\/S0219720016500098","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,19]],"date-time":"2019-09-19T16:42:57Z","timestamp":1568911377000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/S0219720016500098"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,6]]},"references-count":11,"journal-issue":{"issue":"03","published-online":{"date-parts":[[2016,6,14]]},"published-print":{"date-parts":[[2016,6]]}},"alternative-id":["10.1142\/S0219720016500098"],"URL":"https:\/\/doi.org\/10.1142\/s0219720016500098","relation":{},"ISSN":["0219-7200","1757-6334"],"issn-type":[{"type":"print","value":"0219-7200"},{"type":"electronic","value":"1757-6334"}],"subject":[],"published":{"date-parts":[[2016,6]]}}}