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Nucleic Acids Res
2009 Jan 01;37Database issue:D750-4. doi: 10.1093/nar/gkn887.
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SpBase: the sea urchin genome database and web site.
Cameron RA
,
Samanta M
,
Yuan A
,
He D
,
Davidson E
.
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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.
Figure 1. The phylogeny of species from the echinoderm clade discussed in the text. The divergence time of the branches are indicated to the left of the line. All except the most divergent species are regular sea urchins and A. miniata is a sea star and P. flava belongs to Hemichordata, the sister phylum to the echinoderms.
Figure 2. A screen shot of the Gbrowse window for a specific gene model. The BACs and ESTs mapping to the scaffold from which the model originated are displayed. In addition to the sequences, the viewer has access to the actual clone designations and can order them from our facility.
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