{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T19:32:10Z","timestamp":1776108730003,"version":"3.50.1"},"reference-count":53,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2017,4,28]],"date-time":"2017-04-28T00:00:00Z","timestamp":1493337600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["JP16J00129"],"award-info":[{"award-number":["JP16J00129"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["JP16H05879"],"award-info":[{"award-number":["JP16H05879"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>LncRNAs play important roles in various biological processes. Although more than 58\u2009000 human lncRNA genes have been discovered, most known lncRNAs are still poorly characterized. One approach to understanding the functions of lncRNAs is the detection of the interacting RNA target of each lncRNA. Because experimental detections of comprehensive lncRNA\u2013RNA interactions are difficult, computational prediction of lncRNA\u2013RNA interactions is an indispensable technique. However, the high computational costs of existing RNA\u2013RNA interaction prediction tools prevent their application to large-scale lncRNA datasets.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we present \u2018RIblast\u2019, an ultrafast RNA\u2013RNA interaction prediction method based on the seed-and-extension approach. RIblast discovers seed regions using suffix arrays and subsequently extends seed regions based on an RNA secondary structure energy model. Computational experiments indicate that RIblast achieves a level of prediction accuracy similar to those of existing programs, but at speeds over 64 times faster than existing programs.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The source code of RIblast is freely available at https:\/\/github.com\/fukunagatsu\/RIblast.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx287","type":"journal-article","created":{"date-parts":[[2017,4,27]],"date-time":"2017-04-27T15:11:20Z","timestamp":1493305880000},"page":"2666-2674","source":"Crossref","is-referenced-by-count":102,"title":["RIblast: an ultrafast RNA\u2013RNA interaction prediction system based on a seed-and-extension approach"],"prefix":"10.1093","volume":"33","author":[{"given":"Tsukasa","family":"Fukunaga","sequence":"first","affiliation":[{"name":"Faculty of Science and Engineering, Waseda University, Tokyo, Japan"},{"name":"Japan Society for the Promotion of Science, Tokyo, Japan"}]},{"given":"Michiaki","family":"Hamada","sequence":"additional","affiliation":[{"name":"Faculty of Science and Engineering, Waseda University, Tokyo, Japan"},{"name":"Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, Tokyo, Japan"}]}],"member":"286","published-online":{"date-parts":[[2017,4,28]]},"reference":[{"key":"2023020206265421400_btx287-B1","doi-asserted-by":"crossref","first-page":"10099","DOI":"10.1093\/nar\/gku686","article-title":"7SL RNA represses p53 translation by competing with HuR","volume":"42","author":"Abdelmohsen","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020206265421400_btx287-B2","doi-asserted-by":"crossref","first-page":"e05005.","DOI":"10.7554\/eLife.05005","article-title":"Predicting effective microRNA target sites in mammalian mRNAs","volume":"4","author":"Agarwal","year":"2015","journal-title":"Elife"},{"key":"2023020206265421400_btx287-B3","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. 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