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WormBase

Methods for Data Mining and Comparative Genomics

  • Protocol
C. elegans

Part of the book series: Methods in Molecular Biology ((MIMB,volume 351))

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Abstract

WormBase is a comprehensive repository for information on Caenorhabditis elegans and related nematodes. Although the primary web-based interface of WormBase (http://www.wormbase.org/) is familiar to most C. elegans researchers, WormBase also offers powerful data-mining features for addressing questions of comparative genomics, genome structure, and evolution. In this chapter, we focus on data mining at WormBase through the use of flexible web interfaces, custom queries, and scripts. The intended audience includes users wishing to query the database beyond the confines of the web interface or fetch data en masse. No knowledge of programming is necessary or assumed, although users with intermediate skills in the Perl scripting language will be able to utilize additional data-mining approaches.

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References

  1. Stein, L., Sternberg, P., Durbin, R., Thierry-Mieg, J., and Spieth, J. (2001) WormBase: network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Res. 29, 82–86.

    Article  PubMed  CAS  Google Scholar 

  2. Harris, T. W., Lee, R., Schwarz, E., et al. (2003) WormBase: a cross-species database for comparative genomics. Nucleic Acids Res. 31, 133–137.

    Article  PubMed  CAS  Google Scholar 

  3. Harris, T. W., Chen, N., Cunningham, F., et al. (2004) WormBase: a multi-species resource for nematode biology and genomics. Nucleic Acids Res. 32, 411–417.

    Article  Google Scholar 

  4. Chen, N., Harris, T. W., Antoshechkin, I., et al. (2005) WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Nucleic Acids Res. 33, 383–389.

    Article  Google Scholar 

  5. Durbin, R. and Thierry-Mieg, J. (1991) A C. elegans database. Documentation and code available from http://www.acedb.org. Accessed: April 7, 2006.

  6. The C. elegans Genome Sequence Consortium. (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012–2018.

    Article  Google Scholar 

  7. Stein, L. D., Bao, Z., Blasiar, D., et al. (2003) The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PloS Bio. 1, E45.

    Google Scholar 

  8. Fraser, A. G., Kamath, R. S., Zipperlen, P., Martinez-Campos, M., Sohrmann, M., and Ahringer, J. (2000) Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 408, 325–330.

    Article  PubMed  CAS  Google Scholar 

  9. Gonczy, P., Echeverri, C., Oegema, K., et al. (2000) Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III. Nature 408, 331–336.

    Article  PubMed  CAS  Google Scholar 

  10. Kamath, R. S., Fraser, A. G., Dong, Y., et al. (2003) Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421, 231–237.

    Article  PubMed  CAS  Google Scholar 

  11. Sonnichsen, B., Koski, L. B., Walsh, A., et al. (2005) Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature 434, 462–469.

    Article  PubMed  CAS  Google Scholar 

  12. Reboul, J., Vaglio, P., Rual, J. F., et al. (2003) C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat. Genet. 34, 35–41.

    Article  PubMed  Google Scholar 

  13. Lamesch, P., Milstein, S., Hao, T., et al. (2004) C. elegans ORFeome version 3.1: increasing the coverage of ORFeome resources with improved gene predictions. Genome Res. 14, 2064–2069.

    Article  PubMed  CAS  Google Scholar 

  14. Sulston, J. E. and Horvitz, H. R. (1977) Post-embryonic cell lineages of the nematode, Caenorhabditis elegans. Dev. Biol. 56, 110–156.

    Article  PubMed  CAS  Google Scholar 

  15. Sulston, J. E., Schierenberg, E., White, J. G., and Thomson, J. N. (1983) The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev. Biol. 100, 64–119.

    Article  PubMed  CAS  Google Scholar 

  16. White, J. G., Southgate, E., Thomson, J. N., and Brenner, S. (1986). The structure of the nervous system of Caenorhabditis elegans. Philos. Trans. R. Soc. Lond. (B. Biol. Sci.). 314, 1–340.

    Article  Google Scholar 

  17. Additional information on BioMart is available at http://www.ebi.ac.uk/biomart/. Accessed: April 7, 2006.

  18. Stein L. D. and Thierry-Mieg, J. (1998) Scriptable access to the Caenorhabditis elegans genome sequence and other ACEDB databases. Genome Res. 8, 1308–1315.

    PubMed  CAS  Google Scholar 

  19. Stajich, J. E., Block, D., Boulez, K., et al. (2002) The BioPerl toolkit: Perl modules for the life sciences. Genome Res. 12, 1611–1618.

    Article  PubMed  CAS  Google Scholar 

  20. 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.

    Article  PubMed  CAS  Google Scholar 

  21. Dowell, R. D., Jokerst, R. M., Day, A., Eddy, S. R., and Stein L. (2001) The distributed annotation system. BMC Bioinformatics 2, 7 Epub, Oct 10.

    Google Scholar 

  22. Kent, W. J., and Zahler, A. M. (2000) Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Genome Res. 8, 1115–1125.

    Article  Google Scholar 

  23. Schwarz, R.L. and Christiansen, T. (2001). Learning Perl, 2nd Ed., O’Reilly, Sebastapol, CA.

    Google Scholar 

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Author information

Authors and Affiliations

  1. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

    Todd W. Harris & Lincoln D. Stein

Authors
  1. Todd W. Harris
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  2. Lincoln D. Stein
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Editor information

Editors and Affiliations

  1. Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, TN

    Kevin Strange

  2. Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN

    Kevin Strange

  3. Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN

    Kevin Strange

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© 2006 Humana Press Inc.

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Harris, T.W., Stein, L.D. (2006). WormBase. In: Strange, K. (eds) C. elegans. Methods in Molecular Biology, vol 351. Humana Press. https://doi.org/10.1385/1-59745-151-7:31

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  • DOI: https://doi.org/10.1385/1-59745-151-7:31

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-597-2

  • Online ISBN: 978-1-59745-151-2

  • eBook Packages: Springer Protocols

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