Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2005 Jan 1;33(Database issue):D121-4.
doi: 10.1093/nar/gki081.

Rfam: annotating non-coding RNAs in complete genomes

Sam Griffiths-Jones  1 , Simon Moxon, Mhairi Marshall, Ajay Khanna, Sean R Eddy, Alex Bateman
Affiliations

Rfam: annotating non-coding RNAs in complete genomes

Sam Griffiths-Jones et al. Nucleic Acids Res. .

Abstract

Rfam is a comprehensive collection of non-coding RNA (ncRNA) families, represented by multiple sequence alignments and profile stochastic context-free grammars. Rfam aims to facilitate the identification and classification of new members of known sequence families, and distributes annotation of ncRNAs in over 200 complete genome sequences. The data provide the first glimpses of conservation of multiple ncRNA families across a wide taxonomic range. A small number of large families are essential in all three kingdoms of life, with large numbers of smaller families specific to certain taxa. Recent improvements in the database are discussed, together with challenges for the future. Rfam is available on the Web at http://www.sanger.ac.uk/Software/Rfam/ and http://rfam.wustl.edu/.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Rfam genome page for Bacillus anthracis. The table contains a summary of the number of members of each Rfam family in the genome, with the distribution of hits shown on the map.
Figure 2
Figure 2
Taxonomic distribution of Rfam family members in the three kingdoms of life.
See this image and copyright information in PMC

References

    1. Bachellerie J.P., Cavaille,J. and Huttenhofer,A. (2002) The expanding snoRNA world. Biochimie, 84, 775–790. - PubMed
    1. Bartel D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281–297. - PubMed
    1. Storz G., Opdyke,J.A. and Zhang,A. (2004) Controlling mRNA stability and translation with small, noncoding RNAs. Curr. Opin. Microbiol., 7, 140–144. - PubMed
    1. Eddy S.R. (2002) A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinformatics, 3, 18. - PMC - PubMed
    1. Bateman A., Coin,L., Durbin,R., Finn,R.D., Hollich,V., Griffiths-Jones,S., Khanna,A., Marshall,M., Moxon,S., Sonnhammer,E.L. et al. (2003) The Pfam protein families database. Nucleic Acids Res., 32, D138–D141. - PMC - PubMed

Publication types

Substances