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
. 2011 Jan;39(Database issue):D141-5.
doi: 10.1093/nar/gkq1129. Epub 2010 Nov 9.

Rfam: Wikipedia, clans and the "decimal" release

Paul P Gardner  1 , Jennifer Daub, John Tate, Benjamin L Moore, Isabelle H Osuch, Sam Griffiths-Jones, Robert D Finn, Eric P Nawrocki, Diana L Kolbe, Sean R Eddy, Alex Bateman
Affiliations

Rfam: Wikipedia, clans and the "decimal" release

Paul P Gardner et al. Nucleic Acids Res. 2011 Jan.

Abstract

The Rfam database aims to catalogue non-coding RNAs through the use of sequence alignments and statistical profile models known as covariance models. In this contribution, we discuss the pros and cons of using the online encyclopedia, Wikipedia, as a source of community-derived annotation. We discuss the addition of groupings of related RNA families into clans and new developments to the website. Rfam is available on the Web at http://rfam.sanger.ac.uk.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Edits for Wikipedia articles on RNA families. The cumulative number of edits since 1st January 2007 for the 733 Wikipedia articles that are associated with Rfam entries is shown in black. The total number of edits that were reverted or labeled as vandalism is shown in red. To mid-2010, there were just 106 of these. However, some reverted edits may have been well-intentioned but were deemed inappropriate for Wikipedia.
Figure 2.
Figure 2.
An example Stockholm alignment for the UPSK pseudoknot from turnip yellow mosaic virus. The Stockholm alignment format is flexible enough to allow generic mark-up of file information with ‘#=GF' lines, sequence information with ‘#=GS' lines and column information with ‘#=GC' lines. Each is followed by at least a two-letter code giving an indication for what follows e.g. ‘ID' implies ‘identifier', ‘AC' implies ‘accession', ‘AU' implies ‘author', etc. All the commonly used tags are documented in the Wikipedia article for Stockholm alignment (25).
See this image and copyright information in PMC

Similar articles

  • Rfam 11.0: 10 years of RNA families.
    Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A. Burge SW, et al. Nucleic Acids Res. 2013 Jan;41(Database issue):D226-32. doi: 10.1093/nar/gks1005. Epub 2012 Nov 3. Nucleic Acids Res. 2013. PMID: 23125362 Free PMC article.
  • Rfam: an RNA family database.
    Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. Griffiths-Jones S, et al. Nucleic Acids Res. 2003 Jan 1;31(1):439-41. doi: 10.1093/nar/gkg006. Nucleic Acids Res. 2003. PMID: 12520045 Free PMC article.
  • Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families.
    Kalvari I, Argasinska J, Quinones-Olvera N, Nawrocki EP, Rivas E, Eddy SR, Bateman A, Finn RD, Petrov AI. Kalvari I, et al. Nucleic Acids Res. 2018 Jan 4;46(D1):D335-D342. doi: 10.1093/nar/gkx1038. Nucleic Acids Res. 2018. PMID: 29112718 Free PMC article.
  • Customized strategies for discovering distant ncRNA homologs.
    Mosig A, Zhu L, Stadler PF. Mosig A, et al. Brief Funct Genomic Proteomic. 2009 Nov;8(6):451-60. doi: 10.1093/bfgp/elp035. Epub 2009 Sep 24. Brief Funct Genomic Proteomic. 2009. PMID: 19779009 Review.
  • Class-specific prediction of ncRNAs.
    Stadler PF. Stadler PF. Methods Mol Biol. 2014;1097:199-213. doi: 10.1007/978-1-62703-709-9_10. Methods Mol Biol. 2014. PMID: 24639161 Review.
See all similar articles

Cited by

See all "Cited by" articles

References

    1. Holmes I. A probabilistic model for the evolution of RNA structure. BMC Bioinformatics. 2004;5:166. - PMC - PubMed
    1. Do CB, Woods DA, Batzoglou S. CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics. 2006;22:e90–e98. - PubMed
    1. Yao Z, Weinberg Z, Ruzzo WL. CMfinder–a covariance model based RNA motif finding algorithm. Bioinformatics. 2006;22:445–452. - PubMed
    1. Sun Y, Buhler J. Designing secondary structure profiles for fast ncRNA identification. Comput. Syst. Bioinformatics Conf. 2008;7:145–156. - PubMed
    1. Yusuf D, Marz M, Stadler PF, Hofacker IL. Bcheck: a wrapper tool for detecting RNase P RNA genes. BMC Genomics. 2010;11:432. - PMC - PubMed

Publication types

Substances

  NODES
Association 1
coding 2
Community 1
HOME 2
Javascript 1
mac 1
os 16
text 12
twitter 2
web 6