The overall goal of the proposed project is to extend and expand a unique genome data base for sea urchins. The database will be a modest organization incorporating relevant data produced by sea urchin research labs into the annotations and gene models emerging from the work of the Sea Urchin Genome Sequencing Project as managed by the Baylor College of Medicine, Human Genome Sequencing Center and pursued by the members of the Sea Urchin Genome Annotation team. It is specifically intended to fill the void left when the primary annotation is finished and other existing databases are not able to incorporate gene expression data and other specific biological information that can be linked to the genome sequence and gene models. The immediate utility of these data is evidenced by the publication of about 40 research reports in Developmental Biology and Science which emerged from the annotation. One of these reports describes a whole-genome tiling-array that was used to annotate and extend the predicted gene models. In addition the work reported in these publications covers extensive manual gene annotations, another microarray experiment and a wide variety of temporal and spatial gene expression determinations from embryonic stages. It is expected the linkages between much of this experimental data and the primary genomic sequences will be lost or severely degraded over time without the inception of a new database. The new sea urchin genome data base, SpBase will accumulate and maintain the genome sequence, gene annotation and ancillary biological information in a structure suitable for extensive editing, updating and installing of additional features that are specifically useful to the experimentalist using the sea urchin system. The task will be efficiently accomplished through a collaboration that gives us access to software modules from GMOD and expertise from the Wormbase project, a model organism database housed at our home institution.
|Cameron, R Andrew (2014) Tools for sea urchin genomic analysis. Methods Mol Biol 1128:295-310|
|Cameron, R Andrew; Samanta, Manoj; Yuan, Autumn et al. (2009) SpBase: the sea urchin genome database and web site. Nucleic Acids Res 37:D750-4|
|Andrew Cameron, R; Davidson, Eric H (2007) A basal deuterostome genome viewed as a natural experiment. Gene 406:1-7|