WormBase: a multi-species resource for nematode biology and genomics

Abstract

WormBase (http://www.wormbase.org/) is the central data repository for information about Caenorhabditis elegans and related nematodes. As a model organism database, WormBase extends beyond the genomic sequence, integrating experimental results with extensively annotated views of the genome. The WormBase Consortium continues to expand the biological scope and utility of WormBase with the inclusion of large-scale genomic analyses, through active data and literature curation, through new analysis and visualization tools, and through refinement of the user interface. Over the past year, the nearly complete genomic sequence and comparative analyses of the closely related species Caenorhabditis briggsae have been integrated into WormBase, including gene predictions, ortholog assignments and a new synteny viewer to display the relationships between the two species. Extensive site-wide refinement of the user interface now provides quick access to the most frequently accessed resources and a consistent browsing experience across the site. Unified single-page views now provide complete summaries of commonly accessed entries like genes. These advances continue to increase the utility of WormBase for C.elegans researchers, as well as for those researchers exploring problems in functional and comparative genomics in the context of a powerful genetic system.

Figure 1

Navigational elements of the WormBase interface. (A) A static navigational bar at the top of every page gives quick access to the most commonly accessed features of the site. (B) A new search box in the graphical banner enables basic searches from any page. (C) The navigational bar of Report pages shows contextually sensitive options.

Figure 2

The Synteny Viewer shows the relationship of syntenic regions between two genomes. Shown here is an alignment between a gene on chromosome IV of C.elegans and the syntenic region in C.briggsae as determined by the WABA algorithm. The cappuccino colored panel shows the C.elegans contig aligned with C.briggsae, including gene models and the actual WABA alignments. The pink panel shows the corresponding region in C.briggsae aligned with C.elegans. The blue lines connect corresponding locations of the two genomes.

Figure 3

A new Physical Map displays clones generated during the sequencing of C.elegans. Built with the Genome Browser, the Physical Map inherits the same flexibility of user configuration and navigation as that tool.

Figure 4

The revised Gene Report page, which consolidates into a single page information that was previously available across several pages. Many reports in the WormBase site have seen a similar consolidation of information.