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.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
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.
Harris, T. W., Lee, R., Schwarz, E., et al. (2003) WormBase: a cross-species database for comparative genomics. Nucleic Acids Res. 31, 133–137.
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.
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.
Durbin, R. and Thierry-Mieg, J. (1991) A C. elegans database. Documentation and code available from http://www.acedb.org. Accessed: April 7, 2006.
The C. elegans Genome Sequence Consortium. (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012–2018.
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.
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.
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.
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.
Sonnichsen, B., Koski, L. B., Walsh, A., et al. (2005) Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature 434, 462–469.
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.
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.
Sulston, J. E. and Horvitz, H. R. (1977) Post-embryonic cell lineages of the nematode, Caenorhabditis elegans. Dev. Biol. 56, 110–156.
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.
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.
Additional information on BioMart is available at http://www.ebi.ac.uk/biomart/. Accessed: April 7, 2006.
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.
Stajich, J. E., Block, D., Boulez, K., et al. (2002) The BioPerl toolkit: Perl modules for the life sciences. Genome Res. 12, 1611–1618.
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.
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.
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.
Schwarz, R.L. and Christiansen, T. (2001). Learning Perl, 2nd Ed., O’Reilly, Sebastapol, CA.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Humana Press Inc.
About this protocol
Cite this protocol
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
Download citation
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