C. elegans

Volume 351 of the series Methods in Molecular Biology pp 31-50


Methods for Data Mining and Comparative Genomics
  • Todd W. HarrisAffiliated withCold Spring Harbor Laboratory
  • , Lincoln D. SteinAffiliated withCold Spring Harbor Laboratory

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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.

Key Words

WormBase C. elegans AceDB AcePerl bioinformatics data mining comparative genomics