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EchinoBase: Tools for Echinoderm Genome Analyses

  • Gregory A. CaryEmail author
  • R. Andrew Cameron
  • Veronica F. Hinman
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1757)

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.

Key words

Echinoderm Sea urchin Sea star Sea cucumber Brittle star Genome Expression Gene regulatory network (GRN) 

Notes

Acknowledgments

EchinoBase was developed, in part, with support from the NIH (NIH1P41HD071837).

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Gregory A. Cary
    • 1
    Email author
  • R. Andrew Cameron
    • 1
    • 2
  • Veronica F. Hinman
    • 1
  1. 1.Department of Biological Sciences, Mellon InstituteCarnegie Mellon UniversityPittsburghUSA
  2. 2.Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUSA

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