{"metadata":{"_oai":{"id":"oai:ipsj.ixsq.nii.ac.jp:00214045","sets":["1164:5352:10544:10757"]},"path":["10757"],"owner":"44499","recid":"214045","title":["Prediction of RNA secondary structure including pseudoknots for long sequences"],"pubdate":{"attribute_name":"公開日","attribute_value":"2021-11-23"},"_buckets":{"deposit":"2b826be2-a86b-4065-bce0-86bf681c0726"},"_deposit":{"id":"214045","pid":{"type":"depid","value":"214045","revision_id":0},"owners":[44499],"status":"published","created_by":44499},"item_title":"Prediction of RNA secondary structure including pseudoknots for long sequences","author_link":["548398","548399","548400","548401"],"item_titles":{"attribute_name":"タイトル","attribute_value_mlt":[{"subitem_title":"Prediction of RNA secondary structure including pseudoknots for long sequences"},{"subitem_title":"Prediction of RNA secondary structure including pseudoknots for long sequences","subitem_title_language":"en"}]},"item_type_id":"4","publish_date":"2021-11-23","item_4_text_3":{"attribute_name":"著者所属","attribute_value_mlt":[{"subitem_text_value":"Keio University"},{"subitem_text_value":"Osaka Uiversity"}]},"item_4_text_4":{"attribute_name":"著者所属(英)","attribute_value_mlt":[{"subitem_text_value":"Keio University","subitem_text_language":"en"},{"subitem_text_value":"Osaka Uiversity","subitem_text_language":"en"}]},"item_language":{"attribute_name":"言語","attribute_value_mlt":[{"subitem_language":"eng"}]},"item_publisher":{"attribute_name":"出版者","attribute_value_mlt":[{"subitem_publisher":"情報処理学会","subitem_publisher_language":"ja"}]},"publish_status":"0","weko_shared_id":-1,"item_file_price":{"attribute_name":"Billing file","attribute_type":"file","attribute_value_mlt":[{"url":{"url":"https://ipsj.ixsq.nii.ac.jp/record/214045/files/IPSJ-BIO21068005.pdf","label":"IPSJ-BIO21068005.pdf"},"date":[{"dateType":"Available","dateValue":"2023-11-23"}],"format":"application/pdf","billing":["billing_file"],"filename":"IPSJ-BIO21068005.pdf","filesize":[{"value":"547.0 kB"}],"mimetype":"application/pdf","priceinfo":[{"tax":["include_tax"],"price":"0","billingrole":"5"},{"tax":["include_tax"],"price":"0","billingrole":"6"},{"tax":["include_tax"],"price":"0","billingrole":"41"},{"tax":["include_tax"],"price":"0","billingrole":"44"}],"accessrole":"open_date","version_id":"cf1c4a51-f2fe-419b-aef4-f4e43a66a87b","displaytype":"detail","licensetype":"license_note","license_note":"Copyright (c) 2021 by the Information Processing Society of Japan"}]},"item_4_creator_5":{"attribute_name":"著者名","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"Kengo, Sato"}],"nameIdentifiers":[{}]},{"creatorNames":[{"creatorName":"Yuki, Kato"}],"nameIdentifiers":[{}]}]},"item_4_creator_6":{"attribute_name":"著者名(英)","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"Kengo, Sato","creatorNameLang":"en"}],"nameIdentifiers":[{}]},{"creatorNames":[{"creatorName":"Yuki, Kato","creatorNameLang":"en"}],"nameIdentifiers":[{}]}]},"item_4_source_id_9":{"attribute_name":"書誌レコードID","attribute_value_mlt":[{"subitem_source_identifier":"AA12055912","subitem_source_identifier_type":"NCID"}]},"item_4_textarea_12":{"attribute_name":"Notice","attribute_value_mlt":[{"subitem_textarea_value":"SIG Technical Reports are nonrefereed and hence may later appear in any journals, conferences, symposia, etc."}]},"item_resource_type":{"attribute_name":"資源タイプ","attribute_value_mlt":[{"resourceuri":"http://purl.org/coar/resource_type/c_18gh","resourcetype":"technical report"}]},"item_4_source_id_11":{"attribute_name":"ISSN","attribute_value_mlt":[{"subitem_source_identifier":"2188-8590","subitem_source_identifier_type":"ISSN"}]},"item_4_description_7":{"attribute_name":"論文抄録","attribute_value_mlt":[{"subitem_description":"RNA structural elements called pseudoknots are involved in various biological phenomena including ribosomal frameshifts. Because it is infeasible to construct an efficiently computable secondary structure model including pseudoknots, secondary structure prediction methods considering pseudoknots are not yet widely available. We developed IPknot, which uses heuristics to speed up computations, but it has remained difficult to apply it to long sequences because it requires cubic computational time with respect to sequence length and has threshold parameters that need to be manually adjusted. Here, we propose an improvement of IPknot that enables calculation in linear time by employing the LinearPartition model and automatically selects the optimal threshold parameters based on the pseudo-expected accuracy. IPknot showed favorable prediction accuracy across a wide range of conditions in our exhaustive benchmarking, not only for single sequences but also for multiple alignments.","subitem_description_type":"Other"}]},"item_4_description_8":{"attribute_name":"論文抄録(英)","attribute_value_mlt":[{"subitem_description":"RNA structural elements called pseudoknots are involved in various biological phenomena including ribosomal frameshifts. Because it is infeasible to construct an efficiently computable secondary structure model including pseudoknots, secondary structure prediction methods considering pseudoknots are not yet widely available. We developed IPknot, which uses heuristics to speed up computations, but it has remained difficult to apply it to long sequences because it requires cubic computational time with respect to sequence length and has threshold parameters that need to be manually adjusted. Here, we propose an improvement of IPknot that enables calculation in linear time by employing the LinearPartition model and automatically selects the optimal threshold parameters based on the pseudo-expected accuracy. IPknot showed favorable prediction accuracy across a wide range of conditions in our exhaustive benchmarking, not only for single sequences but also for multiple alignments.","subitem_description_type":"Other"}]},"item_4_biblio_info_10":{"attribute_name":"書誌情報","attribute_value_mlt":[{"bibliographicPageEnd":"1","bibliographic_titles":[{"bibliographic_title":"研究報告バイオ情報学（BIO）"}],"bibliographicPageStart":"1","bibliographicIssueDates":{"bibliographicIssueDate":"2021-11-23","bibliographicIssueDateType":"Issued"},"bibliographicIssueNumber":"5","bibliographicVolumeNumber":"2021-BIO-68"}]},"relation_version_is_last":true,"weko_creator_id":"44499"},"id":214045,"updated":"2025-01-19T16:55:30.029824+00:00","links":{},"created":"2025-01-19T01:14:52.928851+00:00"}