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Nucleic Acids Research Advance Access published online on October 25, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn766
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

Rfam: updates to the RNA families database

Paul P. Gardner1,*, Jennifer Daub1, John G. Tate1, Eric P. Nawrocki2, Diana L. Kolbe2, Stinus Lindgreen3, Adam C. Wilkinson1, Robert D. Finn1, Sam Griffiths-Jones4, Sean R. Eddy2 and Alex Bateman1

1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK, 2Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA, 3Center for Bioinformatics, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark and 4Faculty of Life Sciences, The University of Manchester, Manchester M13 9PL, UK

*To whom correspondence should be addressed. Tel: +44 1223 494 983; Fax: +44 1223 494 919; Email: pg5{at}sanger.ac.uk

Received October 1, 2008. Revised October 5, 2008. Accepted October 6, 2008.

Rfam is a collection of RNA sequence families, represented by multiple sequence alignments and covariance models (CMs). The primary aim of Rfam is to annotate new members of known RNA families on nucleotide sequences, particularly complete genomes, using sensitive BLAST filters in combination with CMs. A minority of families with a very broad taxonomic range (e.g. tRNA and rRNA) provide the majority of the sequence annotations, whilst the majority of Rfam families (e.g. snoRNAs and miRNAs) have a limited taxonomic range and provide a limited number of annotations. Recent improvements to the website, methodologies and data used by Rfam are discussed. Rfam is freely available on the Web at http://rfam.sanger.ac.uk/and http://rfam.janelia.org/.


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