Abstract
The echinoderms are a phylum of invertebrate deuterostome animals that constitute important research models for a number of biological disciplines. EchinoBase (www.echinobase.org) is an echinoderm-specific genome database and web information system that provides a platform for the interrogation and exploration of echinoderm genomic data. This chapter outlines the datasets available on EchinoBase; from assembled genomes and genome annotations, to spatial and quantitative expression data, as well as functional genomics datasets. We also highlight the bioinformatic tools available on the website to facilitate rapid inquiries using these data (genome browsers, precompiled BLAST databases, etc.), and suggest optimized strategies for performing these inquiries. We conclude with a perspective on how one could integrate various genomic resources to predict putative noncoding regulatory regions. The available datasets and analyses they permit provide the basic components required for developing an understanding of how echinoderm genomes are regulated, especially during early development, and provides a platform for comparative genomic inquiries among species in this phylum.
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Acknowledgments
EchinoBase was developed, in part, with support from the NIH (NIH1P41HD071837).
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This chapter is dedicated to the memory of Dr. Eric Davidson. A pioneer in understanding the genomic controls of developmental processes, he was a vigorous catalyst for the establishment and curation of echinoderm genome resources, including EchinoBase and its predecessor SpBase.
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Cary, G.A., Cameron, R.A., Hinman, V.F. (2018). EchinoBase: Tools for Echinoderm Genome Analyses. In: Kollmar, M. (eds) Eukaryotic Genomic Databases. Methods in Molecular Biology, vol 1757. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7737-6_12
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DOI: https://doi.org/10.1007/978-1-4939-7737-6_12
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