Annotating Non‐Coding RNAs with Rfam

Sam Griffiths‐Jones1

1 Wellcome Trust Sanger Institute Wellcome Trust Genome Campus, Hinxton, Cambridgeshire
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 12.5
DOI:  10.1002/0471250953.bi1205s9
Online Posting Date:  April, 2005
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Abstract

Non‐coding RNA (ncRNA) genes produce a functional RNA product, rather than a translated protein. The range and importance of such genes is only recently apparent, with known ncRNAs participating in a wide range of structural, regulatory, and catalytic roles within the cell. Like protein‐coding genes, multiple sequence alignments of families of ncRNAs tell us much about their structure and function, and enable the formulation of statistical models for the detection of related sequences. Rfam is a database of families of ncRNAs, represented by structure‐annotated multiple sequence alignments and covariance models.

Keywords: non‐coding RNA; multiple sequence alignment; genome annotation

     
 
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Table of Contents

  • Basic Protocol 1: Finding Members of a Family via the Rfam Web Interface
  • Alternate Protocol 1: Using Rfam and Infernal to Identify ncRNAs in Genomic DNA
  • Guidelines for Understanding Results
  • Commentary
  • Appendix: Rfam Alignment Formats
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

   Bartel, D.P. 2004. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116:281‐297.
   Doudna, J.A. and Cech, T.R. 2002. The chemical repertoire of natural ribozymes. Nature 418:222‐228.
   Durbin, R., Eddy, S., Krogh, A., and Mitchison, G. 1998. Biological sequence analysis: Probabilistic models of proteins and nucleic acids. Cambridge University Press. Cambridge, U.K.
   Griffiths‐Jones, S., Bateman, A., Marshall, M., Khanna, A., and Eddy, S.R. 2003. Rfam: An RNA family database. Nucleic Acids Res. 31:439‐441.
   Griffiths‐Jones, S., Moxon, S., Marshall, M., Khanna, A., Eddy, S.R., and Bateman, A. 2005. Rfam: Annotating non‐coding RNAs in complete genomes. Nucleic Acids Res. 33:D121‐D124.
   Kiss, T. 2002. Small nucleolar RNAs: An abundant group of noncoding RNAs with diverse cellular functions. Cell 109:145‐148.
Internet Resources
   http://www.sanger.ac.uk/Software/Rfam/
  Rfam home pages.
   http://rfam.wustl.edu/
  Rfam FTP sites.
   ftp://ftp.sanger.ac.uk/pub/databases/Rfam/
  INFERNAL home page.
   ftp://ftp.genetics.wustl.edu/pub/eddy/Rfam/
   http://infernal.wustl.edu/
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