An Introduction to RNA Databases

  • Marc P. Hoeppner
  • Lars E. Barquist
  • Paul P. GardnerEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1097)


We present an introduction to RNA databases. The history and technology behind RNA databases are briefly discussed. We examine differing methods of data collection and curation and discuss their impact on both the scope and accuracy of the resulting databases. Finally, we demonstrate these principles through detailed examination of four leading RNA databases: Noncode, miRBase, Rfam, and SILVA.

Key words

ncRNA Database Alignment database Sequence database SILVA Rfam Noncode miRBase 


  1. 1.
    Griffiths-Jones S (2007) Annotating noncoding RNA genes. Annu Rev Genomics Hum Genet 8:279–298PubMedCrossRefGoogle Scholar
  2. 2.
    Hüttenhofer A, Brosius J, Bachellerie JP (2002) RNomics: identification and function of small, non-messenger RNAs. Curr Opin Chem Biol 6:835–843PubMedCrossRefGoogle Scholar
  3. 3.
    Mattick JS, Makunin IV (2006) Non-coding RNA. Hum Mol Genet 15:R17–R29PubMedCrossRefGoogle Scholar
  4. 4.
    Eddy SR (2001) Non-coding RNA genes and the modern RNA world. Nat Rev Genet 2(12):919–929PubMedCrossRefGoogle Scholar
  5. 5.
    Sprinzl M, Vorderwülbecke T, Hartmann T (1985) Compilation of sequences of tRNA genes. Nucleic Acids Res 13: r51–r104PubMedCentralPubMedCrossRefGoogle Scholar
  6. 6.
    Zwieb C, Larsen N (1992) The signal recognition particle (SRP) database. Nucleic Acids Res 20:2207PubMedCentralPubMedCrossRefGoogle Scholar
  7. 7.
    Olsen GJ, Larsen N, Woese CR (1991) The ribosomal RNA database project. Nucleic Acids Res 19:2017–2021PubMedCentralPubMedCrossRefGoogle Scholar
  8. 8.
    Jühling F, Mörl M, Hartmann RK, Sprinzl M, Stadler PF, Pütz J (2009) tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res 37(Database issue):D159–D162PubMedCentralPubMedCrossRefGoogle Scholar
  9. 9.
    Galperin MY, Cochrane GR (2011) The 2011 nucleic acids research database issue and the online molecular biology database collection. Nucleic Acids Res 39(Database issue):D1–D6PubMedCentralPubMedCrossRefGoogle Scholar
  10. 10.
    Huang H-Y, Chang H-Y, Chou C-H, Tseng C-P, Ho S-Y, Yang C-D et al (2009) sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes. Nucleic Acids Res 37(Database issue):D150–D154PubMedCentralPubMedCrossRefGoogle Scholar
  11. 11.
    Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34(Database issue):D140–D144PubMedCentralPubMedCrossRefGoogle Scholar
  12. 12.
    Chalk AM, Warfinge RE, Georgii-Hemming P, Sonnhammer ELL (2005) siRNAdb: a database of siRNA sequences. Nucleic Acids Res 33(Database issue):D131–D134PubMedCentralPubMedCrossRefGoogle Scholar
  13. 13.
    Lestrade L, Weber MJ (2006) snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res 34(Database issue):D158–D162PubMedCentralPubMedCrossRefGoogle Scholar
  14. 14.
    Liu C, Bai B, Skogerbø G, Cai L, Deng W, Zhang Y et al (2005) NONCODE: an integrated knowledge database of non-coding RNAs. Nucleic Acids Res 33(Database issue):D112–D115PubMedCentralPubMedCrossRefGoogle Scholar
  15. 15.
    Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S et al (2011) Rfam: Wikipedia, clans and the “decimal” release. Nucleic Acids Res 39(Database issue):D141–D145PubMedCentralPubMedCrossRefGoogle Scholar
  16. 16.
    Daub J, Gardner PP, Tate J, Ramsköld D, Manske M, Scott WG et al (2008) The RNA WikiProject: community annotation of RNA families. RNA 14(12):2462–2464PubMedCentralPubMedCrossRefGoogle Scholar
  17. 17.
    Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410PubMedGoogle Scholar
  18. 18.
    Gardner PP, Wilm A, Washietl S (2005) A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res 33(8):2433–2439PubMedCentralPubMedCrossRefGoogle Scholar
  19. 19.
    Eddy SR, Durbin R (1994) RNA sequence analysis using covariance models. Nucleic Acids Res 22(11):2079–2088PubMedCentralPubMedCrossRefGoogle Scholar
  20. 20.
    Nawrocki EP, Kolbe DL, Eddy SR (2009) Infernal 1.0: inference of RNA alignments. Bioinformatics 25(10):1335–1337PubMedCentralPubMedCrossRefGoogle Scholar
  21. 21.
    Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25(5):955–964PubMedCentralPubMedCrossRefGoogle Scholar
  22. 22.
    Gardner P, Bateman A, Poole A (2010) SnoPatrol: how many snoRNA genes are there? J Biol 9(1):4PubMedCentralPubMedCrossRefGoogle Scholar
  23. 23.
    Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009) GenBank. Nucleic Acids Res 37(Database issue):D26–D31PubMedCentralPubMedCrossRefGoogle Scholar
  24. 24.
    Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM et al (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1):25–29PubMedCentralPubMedCrossRefGoogle Scholar
  25. 25.
    Griffiths-Jones S (2004) The microRNA Registry. Nucleic Acids Res 32(Database issue):D109–D111PubMedCentralPubMedCrossRefGoogle Scholar
  26. 26.
    Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136(2):215–233PubMedCentralPubMedCrossRefGoogle Scholar
  27. 27.
    Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X et al (2003) A uniform system for microRNA annotation. RNA 9(3):277–279PubMedCentralPubMedCrossRefGoogle Scholar
  28. 28.
    Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, Kim IF et al (2010) NCBI GEO: archive for functional genomics data sets–10 years on. Nucleic Acids Res 39(Database issue):D1005–D1010PubMedCentralPubMedGoogle Scholar
  29. 29.
    Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR (2003) Rfam: an RNA family database. Nucleic Acids Res 31(1):439–441PubMedCentralPubMedCrossRefGoogle Scholar
  30. 30.
    Eddy SR (2008) A probabilistic model of local sequence alignment that simplifies statistical significance estimation. PLoS Comput Biol 4(5):e1000069PubMedCentralPubMedCrossRefGoogle Scholar
  31. 31.
    Eddy SR (2009) A new generation of homology search tools based on probabilistic inference. Genome Inform 23(1):205–211PubMedCrossRefGoogle Scholar
  32. 32.
    Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y et al (2011) Ensembl. Nucleic Acids Res 39(Database issue):D800–D806PubMedCentralPubMedCrossRefGoogle Scholar
  33. 33.
    Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J et al (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35(21):7188–7196PubMedCentralPubMedCrossRefGoogle Scholar
  34. 34.
    Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T, Ussery DW (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35(9):3100–3108PubMedCentralPubMedCrossRefGoogle Scholar
  35. 35.
    Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J et al (2010) Release information: SILVA 104. SILVA: comprehensive ribosomal RNA database. Accessed 7 Apr 2010
  36. 36.
    Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR et al (2011) RNA central: a vision for an international database of RNA sequences. RNA 17(11):1941–1946PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Marc P. Hoeppner
    • 2
  • Lars E. Barquist
    • 3
  • Paul P. Gardner
    • 1
    Email author
  1. 1.School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
  2. 2.Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
  3. 3.Wellcome Trust Genome Campus, Wellcome Trust Sanger InstituteHinxtonUK

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