Annotating Non‐Coding RNAs with Rfam
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
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
- Appendix: Rfam Alignment Formats
- Literature Cited
Figure 12.5.3 The Rfam family page for the nuclear RNase P family.
Figure 12.5.4 The scheme for construction of an Rfam family. The programs cmbuild, cmsearch, and cmalign are components of the INFERNAL software. See text for more detail.
Figure 12.5.5 The Rfam Seed alignment for the U12 minor spliceosomal RNA family.
Figure 12.5.6 The SS_cons line (per‐column) annotation describes the consensus base‐paired secondary structure of a given alignment, encoded as nested sets of brackets.
|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.|
|Rfam home pages.|
|Rfam FTP sites.|
|INFERNAL home page.|