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Nucleic Acids Res. 2009 Jan;37(Database issue):D750-4. doi: 10.1093/nar/gkn887. Epub 2008 Nov 14.

SpBase: the sea urchin genome database and web site.

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Center for Computational Regulatory Genomics, Beckman Institute 139-74, California Institute of Technology, Pasadena, CA 91104, USA.


SpBase is a system of databases focused on the genomic information from sea urchins and related echinoderms. It is exposed to the public through a web site served with open source software ( The enterprise was undertaken to provide an easily used collection of information to directly support experimental work on these useful research models in cell and developmental biology. The information served from the databases emerges from the draft genomic sequence of the purple sea urchin, Strongylocentrotus purpuratus and includes sequence data and genomic resource descriptions for other members of the echinoderm clade which in total span 540 million years of evolutionary time. This version of the system contains two assemblies of the purple sea urchin genome, associated expressed sequences, gene annotations and accessory resources. Search mechanisms for the sequences and the gene annotations are provided. Because the system is maintained along with the Sea Urchin Genome resource, a database of sequenced clones is also provided.

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