Skip to main content
SpringerLink
Log in

An Introduction to RNA Databases

  • Protocol
  • First Online:
Book cover RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1097))

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 139.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 179.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Griffiths-Jones S (2007) Annotating noncoding RNA genes. Annu Rev Genomics Hum Genet 8:279–298

    Article  CAS  PubMed  Google Scholar 

  2. Hüttenhofer A, Brosius J, Bachellerie JP (2002) RNomics: identification and function of small, non-messenger RNAs. Curr Opin Chem Biol 6:835–843

    Article  PubMed  Google Scholar 

  3. Mattick JS, Makunin IV (2006) Non-coding RNA. Hum Mol Genet 15:R17–R29

    Article  CAS  PubMed  Google Scholar 

  4. Eddy SR (2001) Non-coding RNA genes and the modern RNA world. Nat Rev Genet 2(12):919–929

    Article  CAS  PubMed  Google Scholar 

  5. Sprinzl M, Vorderwülbecke T, Hartmann T (1985) Compilation of sequences of tRNA genes. Nucleic Acids Res 13: r51–r104

    Article  PubMed Central  PubMed  Google Scholar 

  6. Zwieb C, Larsen N (1992) The signal recognition particle (SRP) database. Nucleic Acids Res 20:2207

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  7. Olsen GJ, Larsen N, Woese CR (1991) The ribosomal RNA database project. Nucleic Acids Res 19:2017–2021

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  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–D162

    Article  PubMed Central  PubMed  Google Scholar 

  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–D6

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  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–D154

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  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–D144

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  12. Chalk AM, Warfinge RE, Georgii-Hemming P, Sonnhammer ELL (2005) siRNAdb: a database of siRNA sequences. Nucleic Acids Res 33(Database issue):D131–D134

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  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–D162

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  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–D115

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  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–D145

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  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):2462–2464

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  17. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410

    CAS  PubMed  Google Scholar 

  18. Gardner PP, Wilm A, Washietl S (2005) A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res 33(8):2433–2439

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  19. Eddy SR, Durbin R (1994) RNA sequence analysis using covariance models. Nucleic Acids Res 22(11):2079–2088

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  20. Nawrocki EP, Kolbe DL, Eddy SR (2009) Infernal 1.0: inference of RNA alignments. Bioinformatics 25(10):1335–1337

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  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):955–964

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  22. Gardner P, Bateman A, Poole A (2010) SnoPatrol: how many snoRNA genes are there? J Biol 9(1):4

    Article  PubMed Central  PubMed  Google Scholar 

  23. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009) GenBank. Nucleic Acids Res 37(Database issue):D26–D31

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  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):25–29

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  25. Griffiths-Jones S (2004) The microRNA Registry. Nucleic Acids Res 32(Database issue):D109–D111

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  26. Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136(2):215–233

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  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):277–279

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  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–D1010

    PubMed Central  PubMed  Google Scholar 

  29. Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR (2003) Rfam: an RNA family database. Nucleic Acids Res 31(1):439–441

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  30. Eddy SR (2008) A probabilistic model of local sequence alignment that simplifies statistical significance estimation. PLoS Comput Biol 4(5):e1000069

    Article  PubMed Central  PubMed  Google Scholar 

  31. Eddy SR (2009) A new generation of homology search tools based on probabilistic inference. Genome Inform 23(1):205–211

    Article  PubMed  Google Scholar 

  32. Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y et al (2011) Ensembl. Nucleic Acids Res 39(Database issue):D800–D806

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  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):7188–7196

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  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):3100–3108

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  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.http://www.arb-silva.de/documentation/background/release-104/. Accessed 7 Apr 2010

  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):1941–1946

    Article  CAS  PubMed Central  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. School of Biological Sciences, University of Canterbury, Christchurch, New Zealand

    Paul P. Gardner

  2. Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden

    Marc P. Hoeppner

  3. Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, UK

    Lars E. Barquist

Authors
  1. Marc P. Hoeppner
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Lars E. Barquist
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Paul P. Gardner
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Paul P. Gardner .

Editor information

Editors and Affiliations

  1. Center for non-coding RNA in Technology and Health, IKVH University of Copenhagen, Frederiksberg, Denmark

    Jan Gorodkin

  2. University of Washington Dept. Computer Science & Engineering, Seattle, Washington, USA

    Walter L. Ruzzo

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media New York

About this protocol

Cite this protocol

Hoeppner, M.P., Barquist, L.E., Gardner, P.P. (2014). An Introduction to RNA Databases. In: Gorodkin, J., Ruzzo, W. (eds) RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods. Methods in Molecular Biology, vol 1097. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-709-9_6

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-709-9_6

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-708-2

  • Online ISBN: 978-1-62703-709-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation