{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,4]],"date-time":"2024-08-04T02:32:06Z","timestamp":1722738726155},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,10,1]]},"abstract":"Abstract<\/jats:title>\n Summary: With the increasing amount of newly discovered non-coding RNAs, the interactions between RNA molecules become an increasingly important aspect for characterizing their functionality. Many computational tools have been developed to predict the formation of duplexes between two RNAs, either based on single sequences or alignments of homologous sequences. Here, we present RILogo, a program to visualize inter- and intramolecular base pairing between two RNA molecules. The input for RILogo is a pair of structure-annotated sequences or alignments. In the latter case, RILogo displays the alignments in the form of sequence logos, including the mutual information of base paired columns. We also introduce two novel mutual information based measures that weigh the covariance information by the evolutionary distances of the aligned sequences. We show that the new measures have an increased accuracy compared with previous mutual information measures.<\/jats:p>\n Availability and implementation: RILogo is freely available as a stand-alone program and is accessible via a web server at http:\/\/rth.dk\/resources\/rilogo.<\/jats:p>\n Contact: \u00a0pmenzel@gmail.com<\/jats:p>\n Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts461","type":"journal-article","created":{"date-parts":[[2012,7,24]],"date-time":"2012-07-24T02:49:44Z","timestamp":1343098184000},"page":"2523-2526","source":"Crossref","is-referenced-by-count":14,"title":["RILogo: visualizing RNA\u2013RNA interactions"],"prefix":"10.1093","volume":"28","author":[{"given":"Peter","family":"Menzel","sequence":"first","affiliation":[{"name":"1 The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maal\u00f8es Vej 5, Copenhagen DK-2200, 2Center for non-coding RNA in Technology and Health and 3IKVH, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, DK-1870 Frederiksberg, Denmark"}]},{"given":"Stefan E.","family":"Seemann","sequence":"additional","affiliation":[{"name":"1 The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maal\u00f8es Vej 5, Copenhagen DK-2200, 2Center for non-coding RNA in Technology and Health and 3IKVH, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, DK-1870 Frederiksberg, Denmark"},{"name":"1 The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maal\u00f8es Vej 5, Copenhagen DK-2200, 2Center for non-coding RNA in Technology and Health and 3IKVH, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, DK-1870 Frederiksberg, Denmark"}]},{"given":"Jan","family":"Gorodkin","sequence":"additional","affiliation":[{"name":"1 The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maal\u00f8es Vej 5, Copenhagen DK-2200, 2Center for non-coding RNA in Technology and Health and 3IKVH, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, DK-1870 Frederiksberg, Denmark"},{"name":"1 The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maal\u00f8es Vej 5, Copenhagen DK-2200, 2Center for non-coding RNA in Technology and Health and 3IKVH, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, DK-1870 Frederiksberg, Denmark"}]}],"member":"286","published-online":{"date-parts":[[2012,7,23]]},"reference":[{"key":"2023012513143559300_bts461-B1","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1093\/bioinformatics\/16.6.501","article-title":"Phylogenetically enhanced statistical tools for RNA structure prediction","volume":"16","author":"Akmaev","year":"2000","journal-title":"Bioinformatics"},{"key":"2023012513143559300_bts461-B2","doi-asserted-by":"crossref","first-page":"329","DOI":"10.7155\/jgaa.00131","article-title":"Efficient drawing of RNA secondary structure","volume":"10","author":"Auber","year":"2006","journal-title":"J. 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