Commentary | Published:

What everybody should know about the rat genome and its online resources

Nature Genetics volume 40, pages 523527 (2008) | Download Citation

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It has been four years since the original publication of the draft sequence of the rat genome. Five groups are now working together to assemble, annotate and release an updated version of the rat genome. As the prevailing model for physiology, complex disease and pharmacological studies, there is an acute need for the rat's genomic resources to keep pace with the rat's prominence in the laboratory. In this commentary, we describe the current status of the rat genome sequence and the plans for its impending 'upgrade'. We then cover the key online resources providing access to the rat genome, including the new SNP views at Ensembl, the RefSeq and Genes databases at the US National Center for Biotechnology Information, Genome Browser at the University of California Santa Cruz and the disease portals for cardiovascular disease and obesity at the Rat Genome Database.

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References

  1. 1.

    et al. Nature 428, 493–521 (2004).

  2. 2.

    , & Physiol. Genomics 32, 273–282 (2007).

  3. 3.

    STAR Consortium. Nat. Genet. 40, 560–566 (2008).

  4. 4.

    et al. Science 303, 807 (2004).

  5. 5.

    et al. Nucleic Acids Res. 35, D610–D617 (2007).

  6. 6.

    et al. Genome Res. 14, 942–950 (2004).

  7. 7.

    , & in In Silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins (eds. Mulder, N. & Apweiler, R.) 109–113 (Nova Science, New York, 2006).

  8. 8.

    , , & Genome Res. 14, 976–987 (2004).

  9. 9.

    et al. Nat. Genet. 38, 853 (2006).

  10. 10.

    et al. Bioinformatics 22, 509–511 (2006).

  11. 11.

    et al. Genome Res. 14, 160–169 (2004).

  12. 12.

    et al. Genome Res. 14, 742–749 (2004).

  13. 13.

    , , , & Nucleic Acids Res. 35, D658–D662 (2007).

  14. 14.

    , & Nucleic Acids Res. 35, D61–D65 (2007).

  15. 15.

    , , & Nucleic Acids Res. 35, D26–D31 (2007).

  16. 16.

    , , , & Proc. Natl. Acad. Sci. USA 100, 11484–11489 (2003).

  17. 17.

    et al. Genome Res. 12, 996–1006 (2002).

  18. 18.

    et al. Nucleic Acids Res. 36, D773–D779 (2008).

  19. 19.

    , , , & Nucleic Acids Res. 36, D724–D728 (2008).

  20. 20.

    The Uniprot Consortium. Nucleic Acids Res. 35, D193–D197 (2007).

  21. 21.

    & Brief. Bioinform. 7, 256–274 (2006).

  22. 22.

    et al. Nat. Genet. 25, 25–29 (2000).

  23. 23.

    , & Genome Biol. 6, R7 (2005).

  24. 24.

    et al. Nat. Genet. 40, 516–522 (2008).

Download references

Acknowledgements

We thank T. Aitman, N. Hübner and A. Kwitek for helpful comments during the preparation of this manuscript. This work was supported in part by the Intramural Research Program of the US National Institutes of Health, National Library of Medicine. RGD is supported in part by US National Institutes of Health grants HL-64541 and HG-002273. EURATools and the STAR consortium are supported through the Sixth Framework Programme of the European Union, action line LSH-2003-1.1.0-1. The UCSC Genome Browser project is funded by grants from the NHGRI, the Howard Hughes Medical Institute and the US National Cancer Institute. The Phase 2 genome project and SNP discovery at Baylor College of Medicine Human Genome Sequencing Center is funded by NHGRI HG-003273.

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Affiliations

  1. Simon N. Twigger and Howard J. Jacob are at the Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, USA.

    • Simon N Twigger
    •  & Howard J Jacob
  2. Kim D. Pruitt, Donna R. Maglott and Garth Brown are at the National Center for Biotechnology Information, 8600 Rockville Pike, Bethesda, Maryland 20894, USA.

    • Kim D Pruitt
    • , Donna R Maglott
    •  & Garth Brown
  3. Xosé M. Fernández-Suárez and Ewan Birney are at the European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK.

    • Xosé M Fernández-Suárez
    •  & Ewan Birney
  4. Donna Karolchik and Jim Kent are at the University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA.

    • Donna Karolchik
    •  & Jim Kent
  5. Kim C. Worley, George Weinstock and Richard A. Gibbs are at the Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

    • Kim C Worley
    • , George Weinstock
    •  & Richard A Gibbs

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Correspondence to Simon N Twigger.

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https://doi.org/10.1038/ng0508-523

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