WormBase 2007 - PubMed (original) (raw)

. 2008 Jan;36(Database issue):D612-7.

doi: 10.1093/nar/gkm975. Epub 2007 Nov 8.

Igor Antoshechkin, Tamberlyn Bieri, Darin Blasiar, Carol Bastiani, Payan Canaran, Juancarlos Chan, Wen J Chen, Paul Davis, Jolene Fernandes, Tristan J Fiedler, Michael Han, Todd W Harris, Ranjana Kishore, Raymond Lee, Sheldon McKay, Hans-Michael Müller, Cecilia Nakamura, Philip Ozersky, Andrei Petcherski, Gary Schindelman, Erich M Schwarz, Will Spooner, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Karen Yook, Richard Durbin, Lincoln D Stein, John Spieth, Paul W Sternberg

Affiliations

• PMID: 17991679
• PMCID: PMC2238927
• DOI: 10.1093/nar/gkm975

WormBase 2007

Anthony Rogers et al. Nucleic Acids Res. 2008 Jan.

Abstract

WormBase (www.wormbase.org) is the major publicly available database of information about Caenorhabditis elegans, an important system for basic biological and biomedical research. Derived from the initial ACeDB database of C. elegans genetic and sequence information, WormBase now includes the genomic, anatomical and functional information about C. elegans, other Caenorhabditis species and other nematodes. As such, it is a crucial resource not only for C. elegans biologists but the larger biomedical and bioinformatics communities. Coverage of core areas of C. elegans biology will allow the biomedical community to make full use of the results of intensive molecular genetic analysis and functional genomic studies of this organism. Improved search and display tools, wider cross-species comparisons and extended ontologies are some of the features that will help scientists extend their research and take advantage of other nematode species genome sequences.

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Figures

Figure 1.

Syntenic alignments of C. elegans, C. briggsae and C. remanei.

Figure 2.

Expression details of ife-4 shown in genome browser. Cartoon worms show approximate expression location. Mouse over pop-up window (left-center box) gives more details and original image. SAGE tags shown as blue/pink triangles with tag sequence and count. Sequences used in microarray experiments shown as horizontal, orange bar which can be clicked for more details. Gene exons displayed as pink boxes.

Figure 3.

N-Browse can be accessed via the icon on the Gene page (inset). Gene information (left panel) is taken from WormBase. Each gene in the main network window can be clicked to expand the network. Interaction types are colour-coded and can be switched dynamically on or off with the check boxes (lower panel). Search and navigation tools are provided in the top bar.

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