{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T05:29:01Z","timestamp":1777526941217,"version":"3.51.4"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>MicroRNAs (miRNAs) are a group of small, \u223c21 nt long, riboreg-ulators inhibiting gene expression at a post-transcriptional level. Their most distinctive structural feature is the foldback hairpin of their precursor pre-miRNAs. Even though each pre-miRNA deposited in miRBase has its secondary structure already predicted, little is known about the patterns of structural conservation among pre-miRNAs. We address this issue by clustering the human pre-miRNA sequences based on pairwise, sequence and secondary structure alignment using FOLDALIGN, followed by global multiple alignment of obtained clusters by WAR. As a result, the common secondary structure was successfully determined for four FOLDALIGN clusters: the RF00027 structural family of the Rfam database and three clusters with previously undescribed consensus structures.<\/jats:p><jats:p>Availability: \u00a0http:\/\/genome.ku.dk\/resources\/mirclust<\/jats:p><jats:p>Contact: \u00a0gorodkin@genome.ku.dk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn628","type":"journal-article","created":{"date-parts":[[2008,12,6]],"date-time":"2008-12-06T01:14:11Z","timestamp":1228526051000},"page":"291-294","source":"Crossref","is-referenced-by-count":54,"title":["Structural profiles of human miRNA families from pairwise clustering"],"prefix":"10.1093","volume":"25","author":[{"given":"Bogumi\u0142","family":"Kaczkowski","sequence":"first","affiliation":[{"name":"1 Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Frederiksberg C, Denmark, 2Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103 Leipzig, 3Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center of Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, Leipzig, Germany, 4Santa Fe Institute, Santa Fe NM87501, USA and 5Institute of Theoretical Chemistry, University of Vienna, W\u00e4hringerstr. 17, A-1090 Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elfar","family":"Torarinsson","sequence":"additional","affiliation":[{"name":"1 Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Frederiksberg C, Denmark, 2Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103 Leipzig, 3Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center of Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, Leipzig, Germany, 4Santa Fe Institute, Santa Fe NM87501, USA and 5Institute of Theoretical Chemistry, University of Vienna, W\u00e4hringerstr. 17, A-1090 Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kristin","family":"Reiche","sequence":"additional","affiliation":[{"name":"1 Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Frederiksberg C, Denmark, 2Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103 Leipzig, 3Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center of Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, Leipzig, Germany, 4Santa Fe Institute, Santa Fe NM87501, USA and 5Institute of Theoretical Chemistry, University of Vienna, W\u00e4hringerstr. 17, A-1090 Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jakob Hull","family":"Havgaard","sequence":"additional","affiliation":[{"name":"1 Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Frederiksberg C, Denmark, 2Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103 Leipzig, 3Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center of Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, Leipzig, Germany, 4Santa Fe Institute, Santa Fe NM87501, USA and 5Institute of Theoretical Chemistry, University of Vienna, W\u00e4hringerstr. 17, A-1090 Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter F.","family":"Stadler","sequence":"additional","affiliation":[{"name":"1 Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Frederiksberg C, Denmark, 2Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103 Leipzig, 3Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center of Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, Leipzig, Germany, 4Santa Fe Institute, Santa Fe NM87501, USA and 5Institute of Theoretical Chemistry, University of Vienna, W\u00e4hringerstr. 17, A-1090 Vienna, Austria"},{"name":"1 Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Frederiksberg C, Denmark, 2Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103 Leipzig, 3Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center of Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, Leipzig, Germany, 4Santa Fe Institute, Santa Fe NM87501, USA and 5Institute of Theoretical Chemistry, University of Vienna, W\u00e4hringerstr. 17, A-1090 Vienna, Austria"},{"name":"1 Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Frederiksberg C, Denmark, 2Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103 Leipzig, 3Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center of Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, Leipzig, Germany, 4Santa Fe Institute, Santa Fe NM87501, USA and 5Institute of Theoretical Chemistry, University of Vienna, W\u00e4hringerstr. 17, A-1090 Vienna, Austria"},{"name":"1 Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Frederiksberg C, Denmark, 2Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103 Leipzig, 3Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center of Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, Leipzig, Germany, 4Santa Fe Institute, Santa Fe NM87501, USA and 5Institute of Theoretical Chemistry, University of Vienna, W\u00e4hringerstr. 17, A-1090 Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jan","family":"Gorodkin","sequence":"additional","affiliation":[{"name":"1 Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Frederiksberg C, Denmark, 2Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103 Leipzig, 3Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center of Bioinformatics, University of Leipzig, 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