{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T23:04:16Z","timestamp":1773270256917,"version":"3.50.1"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Small nucleolar RNAs are an abundant class of non-coding RNAs that guide chemical modifications of rRNAs, snRNAs and some mRNAs. In the case of many \u2018orphan\u2019 snoRNAs, the targeted nucleotides remain unknown, however. The box H\/ACA subclass determines uridine residues that are to be converted into pseudouridines via specific complementary binding in a well-defined secondary structure configuration that is outside the scope of common RNA (co-)folding algorithms.<\/jats:p>\n               <jats:p>Results: \u00a0RNAsnoop implements a dynamic programming algorithm that computes thermodynamically optimal H\/ACA-RNA interactions in an efficient scanning variant. Complemented by an support vector machine (SVM)-based machine learning approach to distinguish true binding sites from spurious solutions and a system to evaluate comparative information, it presents an efficient and reliable tool for the prediction of H\/ACA snoRNA target sites. We apply RNAsnoop to identify the snoRNAs that are responsible for several of the remaining \u2018orphan\u2019 pseudouridine modifications in human rRNAs, and we assign a target to one of the five orphan H\/ACA snoRNAs in Drosophila.<\/jats:p>\n               <jats:p>Availability: The C source code of RNAsnoop is freely available at http:\/\/www.tbi.univie.ac.at\/\u223chtafer\/RNAsnoop<\/jats:p>\n               <jats:p>Contact: \u00a0htafer@tbi.univie.ac.at<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp680","type":"journal-article","created":{"date-parts":[[2009,12,17]],"date-time":"2009-12-17T03:52:01Z","timestamp":1261021921000},"page":"610-616","source":"Crossref","is-referenced-by-count":53,"title":["<tt>RNAsnoop<\/tt>: efficient target prediction for H\/ACA snoRNAs"],"prefix":"10.1093","volume":"26","author":[{"given":"Hakim","family":"Tafer","sequence":"first","affiliation":[{"name":"1 Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria, 2 Bioinformatics Group, Department of Computer Science, 3 Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, 4 Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, 5 RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlikstra\u00dfe 1,D-04103 Leipzig, Germany and 6 The Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM, USA"},{"name":"1 Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria, 2 Bioinformatics Group, Department of Computer Science, 3 Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, 4 Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, 5 RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlikstra\u00dfe 1,D-04103 Leipzig, Germany and 6 The Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM, USA"},{"name":"1 Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria, 2 Bioinformatics Group, Department of Computer Science, 3 Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, 4 Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, 5 RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlikstra\u00dfe 1,D-04103 Leipzig, Germany and 6 The Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM, USA"}]},{"given":"Stephanie","family":"Kehr","sequence":"additional","affiliation":[{"name":"1 Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria, 2 Bioinformatics Group, Department of Computer Science, 3 Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, 4 Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, 5 RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlikstra\u00dfe 1,D-04103 Leipzig, Germany and 6 The Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM, USA"},{"name":"1 Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria, 2 Bioinformatics Group, Department of Computer Science, 3 Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, 4 Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, 5 RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlikstra\u00dfe 1,D-04103 Leipzig, Germany and 6 The Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM, USA"}]},{"given":"Jana","family":"Hertel","sequence":"additional","affiliation":[{"name":"1 Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria, 2 Bioinformatics Group, Department of Computer Science, 3 Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, 4 Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, 5 RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlikstra\u00dfe 1,D-04103 Leipzig, Germany and 6 The Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM, USA"},{"name":"1 Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria, 2 Bioinformatics Group, Department of Computer Science, 3 Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, 4 Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, 5 RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlikstra\u00dfe 1,D-04103 Leipzig, Germany and 6 The Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM, USA"}]},{"given":"Ivo L.","family":"Hofacker","sequence":"additional","affiliation":[{"name":"1 Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria, 2 Bioinformatics Group, Department of Computer Science, 3 Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, 4 Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, 5 RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlikstra\u00dfe 1,D-04103 Leipzig, Germany and 6 The Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM, USA"}]},{"given":"Peter F.","family":"Stadler","sequence":"additional","affiliation":[{"name":"1 Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria, 2 Bioinformatics Group, Department of Computer Science, 3 Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, 4 Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, 5 RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlikstra\u00dfe 1,D-04103 Leipzig, Germany and 6 The Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,12,16]]},"reference":[{"key":"2023012511003213900_B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. 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Biol."},{"key":"2023012511003213900_B12","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1186\/1471-2105-5-113","article-title":"MUSCLE: a multiple sequence alignment method with reduced time and space complexity","volume":"5","author":"Edgar","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2023012511003213900_B13","doi-asserted-by":"crossref","first-page":"1260","DOI":"10.1038\/emboj.2009.79","article-title":"18S rRNA processing requires base pairings of snR30 H\/ACA snoRNA to eukaryote-specific 18S sequences","volume":"28","author":"Fayet-Lebaron","year":"2009","journal-title":"EMBO J."},{"key":"2023012511003213900_B14","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1186\/1756-0500-1-49","article-title":"Fisher: a program for the detection of H\/ACA snoRNAs using MFE secondary structure prediction and comparative genomics \u2014 assessment and update","volume":"1","author":"Freyhult","year":"2008","journal-title":"BMC Res. 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