Drosophila pp 45-59

Part of the Methods in Molecular Biology book series (MIMB, volume 420) | Cite as

FlyBase

A Database for the Drosophila Research Community
  • Rachel Drysdale
  • the FlyBase Consortium

Abstract

FlyBase (http://flybase.org) is the primary database of integrated genetic and genomic data about the Drosophilidae, of which Drosophila melanogaster is the most extensively studied species. Information in FlyBase originates from a variety of sources ranging from large-scale genome projects to the primary research literature. Data-types include sequence-level gene models, molecular classification of gene product functions, mutant phenotypes, mutant lesions and chromosome aberrations, gene expression patterns, transgene insertions, and anatomical images. Query tools allow interrogation of FlyBase through DNA or protein sequence, by gene or mutant name, or through terms from the several ontologies used to capture functional, phenotypic, and anatomical data. Links between FlyBase and external databases provide extensive opportunity for extending exploration into other model organism databases and resources of biological and molecular information. This review will introduce the FlyBase web server and query tools.

Key Words

FlyBase genome analysis BLAST gene function mutant phenotype comparative genomics biological ontologies database query Drosophila 

References

  1. 1.
    Adams, M. D., Celniker, S. E., Holt, R. A., et al. (2000) The genome sequence of Drosophila melanogaster. Science 287, 2185–2195.CrossRefPubMedGoogle Scholar
  2. 2.
    Celniker, S. E., Wheeler, D. A., Kronmiller, B., et al. (2002) Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence. Genome Biol. 3, R79.CrossRefGoogle Scholar
  3. 3.
    Hoskins, R. A., Smith, C. D., Carlson, J. W., et al. (2002) Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. Genome Biol. 3, R85.CrossRefGoogle Scholar
  4. 4.
    Misra, S., Crosby, M. A., Mungall, C. J., et al. (2002) Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol. 3, R83.CrossRefGoogle Scholar
  5. 5.
    Richards, S., Liu, Y., Bettencourt, B., et al. (2005) Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res. 15, 1–18.CrossRefPubMedGoogle Scholar
  6. 6.
    Crosby, M. A., Goodman, J. L., Strelets, V. B., Zhang, P., Gelbart, W. M. and the FlyBase Consortium (2007) FlyBase: Genomes by the dozen. Nucleic Acids Res. 35, D486–D491.CrossRefPubMedGoogle Scholar
  7. 7.
    Gene Ontology Consortium (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32, D258–D261.CrossRefGoogle Scholar
  8. 8.
    Rubin, D. L., Lewis, S. E., Mungall, C. J., (2006) National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge. OMICS 10, 185–198.CrossRefPubMedGoogle Scholar
  9. 9.
    Eilbeck, K., Lewis, S. E., Mungall, C. J., et al. (2005) The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol. 6, R44.CrossRefPubMedGoogle Scholar
  10. 10.
    Grumbling, G., Strelets, V., and The FlyBase Consortium. (2006) FlyBase: anatomical data, images and queries. Nucleic Acids Res. 34, D484–D488.CrossRefPubMedGoogle Scholar
  11. 11.
    Stein, L. D., Mungall, C., Shu, S., et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Res. 12, 1599–1610.CrossRefPubMedGoogle Scholar
  12. 12.
    Drysdale, R. (2001) Phenotypic Data in FlyBase. Brief. Bioinformatics 2, 68–80.CrossRefPubMedGoogle Scholar
  13. 13.
    Lewis, S. E., Searle, S. M., Harris, N., et al. (2002) Apollo: a sequence annotation editor. Genome Biol. 3, R82.CrossRefGoogle Scholar
  14. 14.
    Lindsley, D. L. and Zimm, G. G. (1992) The Genome of Drosophila melanogaster. Academic Press pp. viii, 1133.Google Scholar
  15. 15.
    Morgan, T. H., Bridges, C. B., and Sturtevant, A. H. (1925) The genetics of Drosophila melanogaster. Biblphia Genet. 2, chapter XXII.Google Scholar
  16. 16.
    Bridges, C. B. and Brehme, K. S. (1944) The mutants of Drosophila melanogaster. Publs. Carnegie Instn. 552.Google Scholar
  17. 17.
    Lindsley, D. L. and Grell, E. H. (1968) Genetic variations of Drosophila melanogaster. Publs. Carnegie Instn. 627.Google Scholar
  18. 18.
    Zhou, P., Emmert, D., and Zhang, P. (2005) Using chado to store genome annotation data, in Current Protocols in Bioinformatics (Baxevanis, A. D. and Davison, D. B., eds.) 2, 9.6.1–9.6.28.Google Scholar

Copyright information

© Humana Press Inc., Totowa, NJ 2008

Authors and Affiliations

  • Rachel Drysdale
    • 1
  • the FlyBase Consortium
  1. 1.Department of GeneticsUniversity of CambridgeCambridgeUK

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