{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,18]],"date-time":"2026-02-18T03:45:09Z","timestamp":1771386309358,"version":"3.50.1"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Long-range RNA-RNA interactions (LRIs) play an important role in viral replication, however, only a few of these interactions are known and only for a small number of viral species. Up to now, it has been impossible to screen a full viral genome for LRIs experimentally or in silico. Most known LRIs are cross-reacting structures (pseudoknots) undetectable by most bioinformatical tools.<\/jats:p>\n               <jats:p>Results: We present LRIscan, a tool for the LRI prediction in full viral genomes based on a multiple genome alignment. We confirmed 14 out of 16 experimentally known and evolutionary conserved LRIs in genome alignments of HCV, Tombusviruses, Flaviviruses and HIV-1. We provide several promising new interactions, which include compensatory mutations and are highly conserved in all considered viral sequences. Furthermore, we provide reactivity plots highlighting the hot spots of predicted LRIs.<\/jats:p>\n               <jats:p>Availability and Implementation: Source code and binaries of LRIscan freely available for download at http:\/\/www.rna.uni-jena.de\/en\/supplements\/lriscan\/, implemented in Ruby\/C\u2002++\u2002and supported on Linux and Windows.<\/jats:p>\n               <jats:p>Contact: \u00a0manja@uni-jena.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw323","type":"journal-article","created":{"date-parts":[[2016,6,11]],"date-time":"2016-06-11T03:54:37Z","timestamp":1465617277000},"page":"2928-2935","source":"Crossref","is-referenced-by-count":14,"title":["Prediction of conserved long-range RNA-RNA interactions in full viral genomes"],"prefix":"10.1093","volume":"32","author":[{"given":"Markus","family":"Fricke","sequence":"first","affiliation":[{"name":"1 Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany"}]},{"given":"Manja","family":"Marz","sequence":"additional","affiliation":[{"name":"1 Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany"},{"name":"2 FLI Leibniz Institute for Age Research, Jena, Germany"}]}],"member":"286","published-online":{"date-parts":[[2016,6,10]]},"reference":[{"key":"2023020113464897700_btw323-B1","doi-asserted-by":"crossref","first-page":"11601","DOI":"10.1074\/jbc.M210291200","article-title":"A novel long distance base-pairing interaction in human immunodeficiency virus type 1 RNA occludes the Gag start codon","volume":"278","author":"Abbink","year":"2003","journal-title":"J. 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