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Clustering Rfam 10.1: Clans, Families, and Classes
Department of Computer Science, Institute of Exact Sciences, University of Brasília, Brasília 70910-900, Brazil
Department of Cellular Biology, Institute of Biology, University of Brasília, Brasília 70910-900, Brazil
Department of Mathematics, University of Brasília, Brasília 70910-900, Brazil
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany
Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, Leipzig D-04103, Germany
Fraunhofer Institut für Zelltherapie und Immunologie–IZI Perlickstraße 1, D-04103 Leipzig, Germany
Institute for Theoretical Chemistry , University of Vienna, Währingerstraße 17, Wien A-1090, Austria
Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark
Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
* Author to whom correspondence should be addressed.
Received: 5 May 2012; in revised form: 4 June 2012 / Accepted: 15 June 2012 / Published: 5 July 2012
Abstract: The Rfam database contains information about non-coding RNAs emphasizing their secondary structures and organizing them into families of homologous RNA genes or functional RNA elements. Recently, a higher order organization of Rfam in terms of the so-called clans was proposed along with its “decimal release”. In this proposition, some of the families have been assigned to clans based on experimental and computational data in order to find related families. In the present work we investigate an alternative classification for the RNA families based on tree edit distance. The resulting clustering recovers some of the Rfam clans. The majority of clans, however, are not recovered by the structural clustering. Instead, they get dispersed into larger clusters, which correspond roughly to well-described RNA classes such as snoRNAs, miRNAs, and CRISPRs. In conclusion, a structure-based clustering can contribute to the elucidation of the relationships among the Rfam families beyond the realm of clans and classes.
Keywords: Rfam; non-coding RNA; secondary structure; clans; clusters
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Lessa, F.A.; Raiol, T.; Brigido, M.M.; Martins Neto, D.S.B.; Walter, M.E.M.T.; Stadler, P.F. Clustering Rfam 10.1: Clans, Families, and Classes. Genes 2012, 3, 378-390.
Lessa FA, Raiol T, Brigido MM, Martins Neto DSB, Walter MEMT, Stadler PF. Clustering Rfam 10.1: Clans, Families, and Classes. Genes. 2012; 3(3):378-390.
Lessa, Felipe A.; Raiol, Tainá; Brigido, Marcelo M.; Martins Neto, Daniele S. B.; Walter, Maria Emília M. T.; Stadler, Peter F. 2012. "Clustering Rfam 10.1: Clans, Families, and Classes." Genes 3, no. 3: 378-390.