{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,17]],"date-time":"2026-01-17T08:40:27Z","timestamp":1768639227530,"version":"3.49.0"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2005,1,1]],"date-time":"2005-01-01T00:00:00Z","timestamp":1104537600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>RNA H-type pseudoknots are ubiquitous pseudoknots that are found in almost all classes of RNA and thought to play very important roles in a variety of biological processes. Detection of these RNA H-type pseudoknots can improve our understanding of RNA structures and their associated functions. However, the currently existing programs for detecting such RNA H-type pseudoknots are still time consuming and sometimes even ineffective. Therefore, efficient and effective tools for detecting the RNA H-type pseudoknots are needed.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this paper, we have adopted a heuristic approach to develop a novel tool, called HPknotter, for efficiently and accurately detecting H-type pseudoknots in an RNA sequence. In addition, we have demonstrated the applicability and effectiveness of HPknotter by testing on some sequences with known H-type pseudoknots. Our approach can be easily extended and applied to other classes of more general pseudoknots.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability<\/jats:title>\n                  <jats:p>The web server of our HPknotter is available for online analysis at http:\/\/bioalgorithm.life.nctu.edu.tw\/HPKNOTTER\/<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Contact<\/jats:title>\n                  <jats:p>cllu@mail.nctu.edu.tw, chiu@cc.nctu.edu.tw<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bti568","type":"journal-article","created":{"date-parts":[[2005,7,1]],"date-time":"2005-07-01T01:46:46Z","timestamp":1120182406000},"page":"3501-3508","source":"Crossref","is-referenced-by-count":39,"title":["A heuristic approach for detecting RNA H-type pseudoknots"],"prefix":"10.1093","volume":"21","author":[{"given":"Chun-Hsiang","family":"Huang","sequence":"first","affiliation":[{"name":"Department of Biological Science and Technology, National Chiao Tung University , Hsinchu 300, Taiwan, Republic of China"}]},{"given":"Chin Lung","family":"Lu","sequence":"additional","affiliation":[{"name":"Department of Biological Science and Technology, National Chiao Tung University , Hsinchu 300, Taiwan, Republic of China"}]},{"given":"Hsien-Tai","family":"Chiu","sequence":"additional","affiliation":[{"name":"Department of Biological Science and Technology, National Chiao Tung University , Hsinchu 300, Taiwan, Republic of China"}]}],"member":"286","published-online":{"date-parts":[[2005,6,30]]},"reference":[{"key":"2023013108401320800_B1","doi-asserted-by":"crossref","first-page":"3035","DOI":"10.1093\/nar\/18.10.3035","volume":"18","year":"1990","journal-title":"Nucleic Acids Res."},{"key":"2023013108401320800_B2","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/S0166-218X(00)00186-4","volume":"104","year":"2000","journal-title":"Discrete Applied Mathematics"},{"key":"2023013108401320800_B3","first-page":"109","year":"1996"},{"key":"2023013108401320800_B4","first-page":"66","volume":"19","year":"2003","journal-title":"Bioinformatics"},{"key":"2023013108401320800_B5","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/1471-2105-3-2","volume":"3","year":"2002","journal-title":"BMC Bioinformatics"},{"key":"2023013108401320800_B6","first-page":"75","year":"1995"},{"key":"2023013108401320800_B7","doi-asserted-by":"crossref","first-page":"1664","DOI":"10.1002\/jcc.10296","volume":"24","year":"2003","journal-title":"J. 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