miRBase:The MicroRNA Sequence Database

  • Sam Griffiths-Jones
Part of the Methods in Molecular Biology™ book series (MIMB, volume 342)


The miRBase Sequence database is the primary repository for published microRNA (miRNA) sequence and annotation data. miRBase provides a user-friendly web interface for miRNA data, allowing the user to search using key words or sequences, trace links to the primary literature referencing the miRNA discoveries, analyze genomic coordinates and context, and mine relationships between miRNA sequences. miRBase also provides a confidential gene-naming service, assigning official miRNA names to novel genes before their publication. The methods outlined in this chapter describe these functions. miRBase is freely available to all at http://microrna.sanger.ac.uk/.

Key Words

MicroRNA homolog gene names noncoding RNA 


  1. 1.
    Griffiths-Jones, S. (2004) The microRNA Registry. Nucleic Acids Res. 32, D109–D111.CrossRefPubMedGoogle Scholar
  2. 2.
    Enright, A. J., John, B., Gaul, U., Tuschl, T., Sander, C., and Marks, D. S. (2003) MicroRNA targets in Drosophila. Genome Biol. 5, R1.CrossRefPubMedGoogle Scholar
  3. 3.
    John, B., Enright, A. J., Aravin, A., Tuschl, T., Sander, C., and Marks, D. S. (2004) Human microRNA targets. PLoS Biol. 2, e363.CrossRefPubMedGoogle Scholar
  4. 4.
    Hubbard, T., Andrews, D., Caccamo, M., et al. (2005) Ensembl 2005. Nucleic Acids Res. 33, D447–D453.CrossRefPubMedGoogle Scholar
  5. 5.
    Ambros, V., Bartel, B., Bartel, D. P., et al. (2003) A uniform system for microRNA annotation. RNA 9, 277–279.CrossRefPubMedGoogle Scholar
  6. 6.
    Bartel, D. P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281–297.CrossRefPubMedGoogle Scholar
  7. 7.
    Altschul, S. F., Madden, T. L., Schaffer, A. A., et al. (1997) Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402.CrossRefPubMedGoogle Scholar
  8. 8.
    Pearson, W. R. (2000) Flexible sequence similarity searching with the FASTA3 program package. Methods Mol. Biol. 132, 185–219.PubMedGoogle Scholar
  9. 9.
    Durbin, R., Eddy, S., Krogh, A., and Mitchison, G. (1998) Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, UK.CrossRefGoogle Scholar
  10. 10.
    Korf, I., Yandell, M., and Bedell, J. (2003) BLAST. O’Reilly & Associates, Sebastopol, CA.Google Scholar

Copyright information

© Humana Press Inc. 2006

Authors and Affiliations

  • Sam Griffiths-Jones
    • 1
  1. 1.Wellcome Trust Sanger InstituteWellcome Trust Genome CampusHinxtonUK

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