The EMBL Nucleotide Sequence and Genome Reviews Databases

  • Peter Sterk
  • Tamara Kulikova
  • Paul Kersey
  • Rolf Apweiler
Part of the Methods in Molecular Biology™ book series (MIMB, volume 406)

Summary

Nucleotide and protein sequence databases are major resources for biological and medical research. This chapter introduces the European Molecular Biology Laboratory (EMBL) Nucleotide Sequence Database, a comprehensive primary data archive for nucleic acid sequences, and Genome Reviews, a secondary database that provides an up-to-date, standardized and comprehensively annotated view of the genomic sequence of selected organisms with completely deciphered genomes. Focusing on plant nucleotide sequences, we demonstrate how these data are accessed, how sequence similarity searches are performed and how we can obtain a wealth of additional information relating to genome sequences using Integr8.

Keywords

Database EMBL Genome Reviews Integr8 SRS sequence analysis BLAST FASTA 

Notes

Acknowledgements

Integr8 and Genome Reviews are funded by the European Commission as the TEMBLOR, contract-no. QLRI-CT-2001000015 under the RTD programme “Quality of Life and Management of Living Resources”.

Reference

  1. 1.
    Kanz, C., Aldebert, P., Althorpe, N., Baker, W., Baldwin, A., Bates, K., Browne, P., van den Broek, A., Castro, M., Cochrane, G., et al. (2005) The EMBL Nucleotide Sequence Database. Nucleic Acids Res. 33, D29–D33.CrossRefPubMedGoogle Scholar
  2. 2.
    Bairoch, A., Apweiler, R., Wu, C. H., Barker, W. C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., et al. (2005) The Universal Protein Resource (UniProt). Nucleic Acids Res. 33, D154–D159.CrossRefPubMedGoogle Scholar
  3. 3.
    Kersey, P., Bower, L., Morris, L., Horne, A., Petryszak, R., Kanz, C., Kanapin, A., Das, U., Michoud, K., Phan, I., et al. (2005) Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. Nucleic Acids Res. 33, D297–D302.CrossRefPubMedGoogle Scholar
  4. 4.
    Leinonen, R., Nardone, F., Oyewole, O., Redaschi, N., and Stoehr, P. (2003) The EMBL sequence version archive. Bioinformatics 19, 1861–1862.CrossRefPubMedGoogle Scholar
  5. 5.
    Dwight, S. S., Balakrishnan, R., Christie, K. R., Costanzo, M. C., Dolinski, K., Engel, S. R., Feierbach, B., Fisk, D. G., Hirschman, J., Hong, E. L., et al. (2004) Saccharomyces genome database: underlying principles and organisation. Brief Bioinform. 5, 9–22.CrossRefPubMedGoogle Scholar
  6. 6.
    Camon, E., Barrell, D., Lee, V., Dimmer, E., and Apweiler, R. (2003) Gene Ontology Annotation Database – an integrated resource of GO annotations to UniProt Knowledgebase. In Silico Biol. 4, 0002.Google Scholar
  7. 7.
    Mulder, N. J., Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Binns, D., Bradley, P., Bork, P., Bucher, P., Cerutti, L., et al. (2005) InterPro, progress and status in 2005. Nucleic Acids Res. 33, D201–D205.CrossRefPubMedGoogle Scholar
  8. 8.
    Lowe, T. M., and Eddy, S. R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964.CrossRefPubMedGoogle Scholar
  9. 9.
    Hubbard, T., Andrews, D., Caccamo, M., Cameron, G., Chen, Y., Clamp, M., Clarke, L., Coates, G., Cox, T., Cunningham, F., et al. (2005) Ensembl 2005. Nucleic Acids Res. 33, D447–D453.CrossRefPubMedGoogle Scholar
  10. 10.
    Petryszak, R., Kretschmann, E., Wieser, D., and Apweiler, R. (2005) The predictive power of the CluSTr database. Bioinformatics 21, 3604–3609.CrossRefPubMedGoogle Scholar
  11. 11.
    Gene Ontology Consortium (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32, D258–D261.CrossRefGoogle Scholar
  12. 12.
    Zdobnov, E. M., Lopez, R., Apweiler, R., and Etzold, T. (2002) The EBI SRS server – recent developments. Bioinformatics 18, 368–373.CrossRefPubMedGoogle Scholar
  13. 13.
    Pearson, W. R. (1994) Using the FASTA program to search protein and DNA sequence databases. Methods Mol. Biol. 24, 307–331.PubMedGoogle Scholar
  14. 14.
    Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402.CrossRefPubMedGoogle Scholar
  15. 15.
    Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680.CrossRefPubMedGoogle Scholar

Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • Peter Sterk
    • 1
  • Tamara Kulikova
    • 1
  • Paul Kersey
    • 1
  • Rolf Apweiler
    • 1
  1. 1.EMBL-Outstation The European Bioinformatics InstituteWellcome Trust Genome CampusHinxtonUK

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