INTRODUCTION

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WormBase is the major public biological database for the nematode Caenorhabditis elegans (Chen et al., 2005). It is meant to be useful to any biologist who wants to use C. elegans, whatever his or her specialty. WormBase contains information about the genomic sequence of C. elegans, its genes and their products, and its higher-level traits such as gene expression patterns and neuronal connectivity. Also, WormBase contains sequence and gene structures of C. briggsae and C. remanei, two closely related worms. These data are interconnected, so that a search beginning with one object (such as a gene) can be directed to related objects of a different type (such as the DNA sequence of the gene, or the cells in which the gene is active). One can also do searches for complex data sets.

WormBase is constantly being changed and expanded, both by curation of newly available data and by modifications to the user interface. The entire database is updated and rebuilt into a new release every 3 weeks throughout the year, in releases named "WSnnn" (with "nnn" being 147 as of this writing). To give bioinformaticians reproducible data sets for their analyses, each tenth release is made permanently available as a frozen online archive, roughly once every seven months. Releases WS100 through WS150 have been archived so far. All of the information in this chapter is based on the version of WormBase available in September, 2005 (WS147 release; BioPerl/Generic Model Organism Database software).

The protocols described in this chapter include the following: general searches of WormBase with single search terms; studying a gene, sequence, or protein with its individual web page, or with the Genome Browser; searching for proteins by BLAST hits, sequence motifs, or Gene Ontology terms; aligning C. elegans with C. briggsae genomic sequences; detailed, user-customized searches with WormMart or AceDB Query Language; batch downloads of many sequences at once; identifying the genomic regions, genetic contents, or molecular clones spanning a defined chromosomal interval; electronic PCR; finding expression patterns, and the cell types or developmental origins from which these patterns arise; and searching for genome-wide RNAi results yielding particular phenotypes. Some advice is also provided for installing and running WormBase on a local computer.