{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,12]],"date-time":"2025-12-12T13:20:44Z","timestamp":1765545644026},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,1,15]]},"abstract":"Abstract<\/jats:title>\n Motivation: Small nucleolar RNAs (snoRNAs) are an abundant class of non-coding RNAs with a wide variety of cellular functions including chemical modification of RNA, telomere maintanance, pre-rRNA processing and regulatory activities in alternative splicing. The main role of box C\/D snoRNAs is to determine the targets for 2\u2032-O-ribose methylation, which is important for rRNA maturation and splicing regulation of some mRNAs. The targets are still unknown, however, for many \u2018orphan\u2019 snoRNAs. While a fast and efficient target predictor for box H\/ACA snoRNAs is available, no comparable tool exists for box C\/D snoRNAs, even though they bind to their targets in a much less complex manner.<\/jats:p>\n Results: \u00a0PLEXY is a dynamic programming algorithm that computes thermodynamically optimal interactions of a box C\/D snoRNA with a putative target RNA. Implemented as scanner for large input sequences and equipped with filters on the duplex structure, PLEXY is an efficient and reliable tool for the prediction of box C\/D snoRNA target sites.<\/jats:p>\n Availability: The perl script PLEXY is freely available at http:\/\/www.bioinf.uni-leipzig.de\/Software\/PLEXY.<\/jats:p>\n Contact: \u00a0steffi@bioinf.uni-leipzig.de<\/jats:p>\n Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq642","type":"journal-article","created":{"date-parts":[[2010,11,14]],"date-time":"2010-11-14T01:26:18Z","timestamp":1289697978000},"page":"279-280","source":"Crossref","is-referenced-by-count":61,"title":["PLEXY<\/tt>: efficient target prediction for box C\/D snoRNAs"],"prefix":"10.1093","volume":"27","author":[{"given":"Stephanie","family":"Kehr","sequence":"first","affiliation":[{"name":"1 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, Germany, 2Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria, 3Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D-04103 Leipzig, 4RNomics Group, Fraunhofer Institute Cell Therapy and Immunology, Perlickstrasse 1, Leipzig, Germany, 5Center for non-coding RNAs in Technology and Health (RTH), University of Copenhagen, Copenhagen, Denmark and 6The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA"}]},{"given":"Sebastian","family":"Bartschat","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, Germany, 2Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria, 3Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D-04103 Leipzig, 4RNomics Group, Fraunhofer Institute Cell Therapy and Immunology, Perlickstrasse 1, Leipzig, Germany, 5Center for non-coding RNAs in Technology and Health (RTH), University of Copenhagen, Copenhagen, Denmark and 6The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA"}]},{"given":"Peter F.","family":"Stadler","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, Germany, 2Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria, 3Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D-04103 Leipzig, 4RNomics Group, Fraunhofer Institute Cell Therapy and Immunology, Perlickstrasse 1, Leipzig, Germany, 5Center for non-coding RNAs in Technology and Health (RTH), University of Copenhagen, Copenhagen, Denmark and 6The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA"},{"name":"1 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, Germany, 2Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria, 3Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D-04103 Leipzig, 4RNomics Group, Fraunhofer Institute Cell Therapy and Immunology, Perlickstrasse 1, Leipzig, Germany, 5Center for non-coding RNAs in Technology and Health (RTH), University of Copenhagen, Copenhagen, Denmark and 6The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA"},{"name":"1 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, Germany, 2Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria, 3Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D-04103 Leipzig, 4RNomics Group, Fraunhofer Institute Cell Therapy and Immunology, Perlickstrasse 1, Leipzig, Germany, 5Center for non-coding RNAs in Technology and Health (RTH), University of Copenhagen, Copenhagen, Denmark and 6The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA"},{"name":"1 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, Germany, 2Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria, 3Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D-04103 Leipzig, 4RNomics Group, Fraunhofer Institute Cell Therapy and Immunology, Perlickstrasse 1, Leipzig, Germany, 5Center for non-coding RNAs in Technology and Health (RTH), University of Copenhagen, Copenhagen, Denmark and 6The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA"},{"name":"1 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, Germany, 2Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria, 3Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D-04103 Leipzig, 4RNomics Group, Fraunhofer Institute Cell Therapy and Immunology, Perlickstrasse 1, Leipzig, Germany, 5Center for non-coding RNAs in Technology and Health (RTH), University of Copenhagen, Copenhagen, Denmark and 6The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA"},{"name":"1 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, Germany, 2Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria, 3Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D-04103 Leipzig, 4RNomics Group, Fraunhofer Institute Cell Therapy and Immunology, Perlickstrasse 1, Leipzig, Germany, 5Center for non-coding RNAs in Technology and Health (RTH), University of Copenhagen, Copenhagen, Denmark and 6The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA"}]},{"given":"Hakim","family":"Tafer","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107 Leipzig, Germany, 2Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria, 3Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D-04103 Leipzig, 4RNomics Group, Fraunhofer Institute Cell Therapy and Immunology, Perlickstrasse 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