{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T00:15:08Z","timestamp":1773274508495,"version":"3.50.1"},"reference-count":68,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2145,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Predicting RNA\u2013RNA interactions is essential for determining the function of putative non-coding RNAs. Existing methods for the prediction of interactions are all based on single sequences. Since comparative methods have already been useful in RNA structure determination, we assume that conserved RNA\u2013RNA interactions also imply conserved function. Of these, we further assume that a non-negligible amount of the existing RNA\u2013RNA interactions have also acquired compensating base changes throughout evolution. We implement a method, PETcofold, that can take covariance information in intra-molecular and inter-molecular base pairs into account to predict interactions and secondary structures of two multiple alignments of RNA sequences.<\/jats:p>\n               <jats:p>Results: \u00a0PETcofold's ability to predict RNA\u2013RNA interactions was evaluated on a carefully curated dataset of 32 bacterial small RNAs and their targets, which was manually extracted from the literature. For evaluation of both RNA\u2013RNA interaction and structure prediction, we were able to extract only a few high-quality examples: one vertebrate small nucleolar RNA and four bacterial small RNAs. For these we show that the prediction can be improved by our comparative approach. Furthermore, PETcofold was evaluated on controlled data with phylogenetically simulated sequences enriched for covariance patterns at the interaction sites. We observed increased performance with increased amounts of covariance.<\/jats:p>\n               <jats:p>Availability: The program PETcofold is available as source code and can be downloaded from http:\/\/rth.dk\/resources\/petcofold.<\/jats:p>\n               <jats:p>Contact: \u00a0gorodkin@rth.dk; backofen@informatik.uni-freiburg.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq634","type":"journal-article","created":{"date-parts":[[2010,11,19]],"date-time":"2010-11-19T03:58:31Z","timestamp":1290139111000},"page":"211-219","source":"Crossref","is-referenced-by-count":51,"title":["PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences"],"prefix":"10.1093","volume":"27","author":[{"given":"Stefan E.","family":"Seemann","sequence":"first","affiliation":[{"name":"1 Center for non-coding RNA in Technology and Health, 2IBHV, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, 1870, Denmark, 3Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, 79110, Germany 4Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna and University of Veterinary Medicine, Dr. Bohr-Gasse 9, Vienna, 1030, Austria and 5Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Albertstrasse 19, Freiburg, 79104, Germany"},{"name":"1 Center for non-coding RNA in Technology and Health, 2IBHV, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, 1870, Denmark, 3Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, 79110, Germany 4Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna and University of Veterinary Medicine, Dr. Bohr-Gasse 9, Vienna, 1030, Austria and 5Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Albertstrasse 19, Freiburg, 79104, Germany"}]},{"given":"Andreas S.","family":"Richter","sequence":"additional","affiliation":[{"name":"1 Center for non-coding RNA in Technology and Health, 2IBHV, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, 1870, Denmark, 3Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, 79110, Germany 4Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna and University of Veterinary Medicine, Dr. Bohr-Gasse 9, Vienna, 1030, Austria and 5Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Albertstrasse 19, Freiburg, 79104, Germany"}]},{"given":"Tanja","family":"Gesell","sequence":"additional","affiliation":[{"name":"1 Center for non-coding RNA in Technology and Health, 2IBHV, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, 1870, Denmark, 3Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, 79110, Germany 4Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna and University of Veterinary Medicine, Dr. Bohr-Gasse 9, Vienna, 1030, Austria and 5Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Albertstrasse 19, Freiburg, 79104, Germany"}]},{"given":"Rolf","family":"Backofen","sequence":"additional","affiliation":[{"name":"1 Center for non-coding RNA in Technology and Health, 2IBHV, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, 1870, Denmark, 3Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, 79110, Germany 4Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna and University of Veterinary Medicine, Dr. Bohr-Gasse 9, Vienna, 1030, Austria and 5Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Albertstrasse 19, Freiburg, 79104, Germany"},{"name":"1 Center for non-coding RNA in Technology and Health, 2IBHV, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, 1870, Denmark, 3Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, 79110, Germany 4Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna and University of Veterinary Medicine, Dr. Bohr-Gasse 9, Vienna, 1030, Austria and 5Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Albertstrasse 19, Freiburg, 79104, Germany"},{"name":"1 Center for non-coding RNA in Technology and Health, 2IBHV, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, 1870, Denmark, 3Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, 79110, Germany 4Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna and University of Veterinary Medicine, Dr. Bohr-Gasse 9, Vienna, 1030, Austria and 5Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Albertstrasse 19, Freiburg, 79104, Germany"}]},{"given":"Jan","family":"Gorodkin","sequence":"additional","affiliation":[{"name":"1 Center for non-coding RNA in Technology and Health, 2IBHV, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, 1870, Denmark, 3Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, 79110, Germany 4Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna and University of Veterinary Medicine, Dr. Bohr-Gasse 9, Vienna, 1030, Austria and 5Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Albertstrasse 19, Freiburg, 79104, Germany"},{"name":"1 Center for non-coding RNA in Technology and Health, 2IBHV, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, 1870, Denmark, 3Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, 79110, Germany 4Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna and University of Veterinary Medicine, Dr. Bohr-Gasse 9, Vienna, 1030, Austria and 5Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Albertstrasse 19, Freiburg, 79104, Germany"}]}],"member":"286","published-online":{"date-parts":[[2010,11,18]]},"reference":[{"key":"2023012512171738500_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. Comput. 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Mol. Evol."},{"key":"2023012512171738500_B16","first-page":"2433","volume":"33","author":"Gardner","year":"2005","journal-title":"A benchmark of multiple sequence alignment programs upon structural RNAs."},{"key":"2023012512171738500_B17","doi-asserted-by":"crossref","first-page":"D136","DOI":"10.1093\/nar\/gkn766","article-title":"Rfam: updates to the RNA families database","volume":"37","author":"Gardner","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012512171738500_B18","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1006\/jmbi.1995.0608","article-title":"An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints","volume":"254","author":"Gaspin","year":"1995","journal-title":"J. Mol. Biol."},{"key":"2023012512171738500_B19","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1038\/sj.emboj.7600058","article-title":"Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator","volume":"23","author":"Geissmann","year":"2004","journal-title":"EMBO J."},{"key":"2023012512171738500_B20","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1093\/bioinformatics\/bti812","article-title":"In silico sequence evolution with site-specific interactions along phylogenetic trees","volume":"22","author":"Gesell","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012512171738500_B21","doi-asserted-by":"crossref","first-page":"2135","DOI":"10.1093\/nar\/29.10.2135","article-title":"Discovering common stem-loop motifs in unaligned RNA sequences","volume":"29","author":"Gorodkin","year":"2001","journal-title":"Nucleic Acids 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broadly distributed in enteric bacteria but have diverged in size and sequence","volume":"37","author":"Horler","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012512171738500_B26","doi-asserted-by":"crossref","first-page":"2646","DOI":"10.1093\/bioinformatics\/btp481","article-title":"Partition function and base pairing probabilities for RNA-RNA interaction prediction","volume":"25","author":"Huang","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012512171738500_B27","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1093\/bioinformatics\/btp635","article-title":"Target prediction and a statistical sampling algorithm for RNA-RNA interaction","volume":"26","author":"Huang","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012512171738500_B28","doi-asserted-by":"crossref","first-page":"2943","DOI":"10.1093\/emboj\/20.11.2943","article-title":"Rnomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs 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history","volume":"15","author":"Knudsen","year":"1999","journal-title":"Bioinformatics"},{"key":"2023012512171738500_B32","doi-asserted-by":"crossref","first-page":"3423","DOI":"10.1093\/nar\/gkg614","article-title":"Pfold: RNA secondary structure prediction using stochastic context-free grammars","volume":"31","author":"Knudsen","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012512171738500_B33","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1093\/bioinformatics\/btp154","article-title":"Local RNA structure alignment with incomplete sequence","volume":"25","author":"Kolbe","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012512171738500_B34","doi-asserted-by":"crossref","first-page":"D158","DOI":"10.1093\/nar\/gkj002","article-title":"snoRNA-LBME-db, a comprehensive database of human H\/ACA and C\/D box snoRNAs","volume":"34","author":"Lestrade","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012512171738500_B35","doi-asserted-by":"crossref","first-page":"2178","DOI":"10.1101\/gr.1224503","article-title":"OrthoMCL: identification of ortholog groups for eukaryotic genomes","volume":"13","author":"Li","year":"2003","journal-title":"Genome Res."},{"key":"2023012512171738500_B36","first-page":"442","article-title":"Comparison of the predicted and observed secondary structure of T4 phage lysozyme","volume":"405","author":"Matthews","year":"1975","journal-title":"Biochem. Biophys. Acta"},{"key":"2023012512171738500_B37","doi-asserted-by":"crossref","first-page":"2075","DOI":"10.1261\/rna.1556009","article-title":"The tedious task of finding homologous noncoding RNA genes","volume":"15","author":"Menzel","year":"2009","journal-title":"RNA"},{"key":"2023012512171738500_B38","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1073\/pnas.0706729105","article-title":"Specific expression of long noncoding RNAs in the mouse brain","volume":"105","author":"Mercer","year":"2008","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012512171738500_B39","doi-asserted-by":"crossref","first-page":"1177","DOI":"10.1093\/bioinformatics\/btl024","article-title":"Thermodynamics of RNA-RNA binding","volume":"22","author":"M\u00fcckstein","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012512171738500_B40","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1007\/978-3-540-70600-7_9","article-title":"Translational control by RNA-RNA interaction: improved computation of RNA-RNA binding thermodynamics","volume-title":"Bioinformatics Research and Development","author":"M\u00fcckstein","year":"2008"},{"key":"2023012512171738500_B41","first-page":"92","article-title":"IRIS: intermolecular RNA interaction search","volume":"15","author":"Pervouchine","year":"2004","journal-title":"Genome Inform."},{"key":"2023012512171738500_B42","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1101\/gr.4200206","article-title":"Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome","volume":"16","author":"Ravasi","year":"2006","journal-title":"Genome Res."},{"key":"2023012512171738500_B43","doi-asserted-by":"crossref","first-page":"1507","DOI":"10.1261\/rna.5248604","article-title":"Fast and effective prediction of microRNA\/target duplexes","volume":"10","author":"Rehmsmeier","year":"2004","journal-title":"RNA"},{"key":"2023012512171738500_B44","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/bioinformatics\/btp609","article-title":"Seed-based IntaRNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1","volume":"26","author":"Richter","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012512171738500_B45","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/1748-7188-5-5","article-title":"Fast prediction of RNA-RNA interaction","volume":"5","author":"Salari","year":"2010","journal-title":"Algorithms Mol. Biol."},{"key":"2023012512171738500_B46","first-page":"473","article-title":"Time and space efficient RNA-RNA interaction prediction via sparse folding","volume-title":"Proceedings of RECOMB 2010","author":"Salari","year":"2010"},{"key":"2023012512171738500_B47","doi-asserted-by":"crossref","first-page":"6355","DOI":"10.1093\/nar\/gkn544","article-title":"Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments","volume":"36","author":"Seemann","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012512171738500_B48","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1186\/1748-7188-5-22","article-title":"Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions","volume":"5","author":"Seemann","year":"2010","journal-title":"Algorithms Mol. Biol."},{"key":"2023012512171738500_B49","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1038\/nature08756","article-title":"The primary transcriptome of the major human pathogen Helicobacter pylori","volume":"464","author":"Sharma","year":"2010","journal-title":"Nature"},{"key":"2023012512171738500_B50","doi-asserted-by":"crossref","first-page":"2657","DOI":"10.1093\/bioinformatics\/btn193","article-title":"RNAplex: a fast tool for RNA-RNA interaction search","volume":"24","author":"Tafer","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012512171738500_B51","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1002\/bies.20544","article-title":"The relationship between non-protein-coding DNA and eukaryotic complexity","volume":"29","author":"Taft","year":"2007","journal-title":"Bioessays"},{"key":"2023012512171738500_B52","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1038\/nature05874","article-title":"Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project","volume":"447","author":"The ENCODE Project Consortium","year":"2007","journal-title":"Nature"},{"key":"2023012512171738500_B53","doi-asserted-by":"crossref","first-page":"885","DOI":"10.1101\/gr.5226606","article-title":"Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure","volume":"16","author":"Torarinsson","year":"2006","journal-title":"Genome Res."},{"key":"2023012512171738500_B54","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1101\/gr.6887408","article-title":"Comparative genomics beyond sequence based alignments: RNA structures in the ENCODE regions","volume":"18","author":"Torarinsson","year":"2008","journal-title":"Genome Res."},{"key":"2023012512171738500_B55","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1016\/S1097-2765(00)80161-6","article-title":"Modification of U6 spliceosomal RNA is guided by other small RNAs","volume":"2","author":"Tycowski","year":"1998","journal-title":"Mol. 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