{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,19]],"date-time":"2026-03-19T20:03:19Z","timestamp":1773950599635,"version":"3.50.1"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Currently, the best RNA\u2013RNA interaction prediction tools are based on approaches that consider both the inter- and intramolecular interactions of hybridizing RNAs. While accurate, these methods are too slow and memory-hungry to be employed in genome-wide RNA target scans. Alternative methods neglecting intramolecular structures are fast enough for genome-wide applications, but are too inaccurate to be of much practical use.<\/jats:p>\n               <jats:p>Results: A new approach for RNA\u2013RNA interaction was developed, with a prediction accuracy that is similar to that of algorithms that explicitly consider intramolecular structures, but running at least three orders of magnitude faster than RNAup. This is achieved by using a combination of precomputed accessibility profiles with an approximate energy model. This approach is implemented in the new version of RNAplex. The software also provides a variant using multiple sequences alignments as input, resulting in a further increase in specificity.<\/jats:p>\n               <jats:p>Availability: \u00a0RNAplex is available at www.bioinf.uni-leipzig.de\/Software\/RNAplex.<\/jats:p>\n               <jats:p>Contact: \u00a0htafer@bioinf.uni-leipzig.de; ivo@tbi.univie.ac.at<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics Online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr281","type":"journal-article","created":{"date-parts":[[2011,5,19]],"date-time":"2011-05-19T02:22:22Z","timestamp":1305771742000},"page":"1934-1940","source":"Crossref","is-referenced-by-count":47,"title":["Fast accessibility-based prediction of RNA\u2013RNA interactions"],"prefix":"10.1093","volume":"27","author":[{"given":"Hakim","family":"Tafer","sequence":"first","affiliation":[]},{"given":"Fabian","family":"Amman","sequence":"additional","affiliation":[]},{"given":"Florian","family":"Eggenhofer","sequence":"additional","affiliation":[]},{"given":"Peter F.","family":"Stadler","sequence":"additional","affiliation":[]},{"given":"Ivo L.","family":"Hofacker","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2011,5,18]]},"reference":[{"key":"2023012712454075100_B1","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1089\/cmb.2006.13.267","article-title":"RNA-RNA interaction prediction and antisense RNA target search","volume":"13","author":"Alkan","year":"2006","journal-title":"J. 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