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Nucleic Acids Research Advance Access originally published online on November 14, 2008
Nucleic Acids Research 2009 37(Database issue):D750-D754; doi:10.1093/nar/gkn887
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Nucleic Acids Research, 2009, Vol. 37, Database issue D750-D754
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

SpBase: the sea urchin genome database and web site

R. Andrew Cameron*, Manoj Samanta, Autumn Yuan, Dong He and Eric Davidson

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

*To whom correspondence should be addressed. Tel: +626 395 8421; Fax: +626 795 3382; Email: acameron{at}caltech.edu

Received October 19, 2008. Accepted October 20, 2008.

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 (http://spbase.org/). 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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