{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T13:36:04Z","timestamp":1781616964248,"version":"3.54.5"},"reference-count":122,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2016,11,24]],"date-time":"2016-11-24T00:00:00Z","timestamp":1479945600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100019601","name":"Biomolecular Interaction Centre","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100019601","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Rutherford Discovery Fellowships"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The aim of this study is to assess the performance of RNA\u2013RNA interaction prediction tools for all domains of life.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Minimum free energy (MFE) and alignment methods constitute most of the current RNA interaction prediction algorithms. The MFE tools that include accessibility (i.e. RNAup, IntaRNA and RNAplex) to the final predicted binding energy have better true positive rates (TPRs) with a high positive predictive values (PPVs) in all datasets than other methods. They can also differentiate almost half of the native interactions from background. The algorithms that include effects of internal binding energies to their model and alignment methods seem to have high TPR but relatively low associated PPV compared to accessibility based methods.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>We shared our wrapper scripts and datasets at Github (github.com\/UCanCompBio\/RNA_Interactions_Benchmark). All parameters are documented for personal use.<\/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\/btw728","type":"journal-article","created":{"date-parts":[[2016,11,16]],"date-time":"2016-11-16T20:05:49Z","timestamp":1479326749000},"page":"988-996","source":"Crossref","is-referenced-by-count":66,"title":["A comprehensive benchmark of RNA\u2013RNA interaction prediction tools for all domains of life"],"prefix":"10.1093","volume":"33","author":[{"given":"Sinan U\u011fur","family":"Umu","sequence":"first","affiliation":[{"name":"School of Biological Sciences, University of Canterbury, Christchurch, New Zealand"},{"name":"Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul P","family":"Gardner","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, University of Canterbury, Christchurch, New Zealand"},{"name":"Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand"},{"name":"Bio-Protection Research Centre, University of Canterbury, Christchurch, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,12,30]]},"reference":[{"key":"2023020205011916900_btw728-B1","doi-asserted-by":"crossref","first-page":"758","DOI":"10.1016\/j.cub.2008.04.042","article-title":"Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome","volume":"18","author":"Addo-Quaye","year":"2008","journal-title":"Curr. 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