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Tools for Sea Urchin Genomic Analysis

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Developmental Biology of the Sea Urchin and Other Marine Invertebrates

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1128))

Abstract

The Sea Urchin Genome Project Web site, SpBase (http://SpBase.org), in association with a suite of publicly available sequence comparison tools provides a platform from which to analyze genes and genomic sequences of sea urchin. This information system is specifically designed to support laboratory bench studies in cell and molecular biology. In particular these tools and datasets have supported the description of the gene regulatory networks of the purple sea urchin S. purpuratus. This chapter details methods to undertake in the first steps to find genes and noncoding regulatory sequences for further analysis.

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Acknowledgements

The genomic information system described here was supported by National Institutes of Health, the National Institute of Child Health and Human Development (R01HD056016); the National Center for Research Resources, Division of Comparative Medicine (RR015044); and the Beckman Institute. I thank Autumn Yuan, Parul Kudtarkar, Ung-Jin Kim, and David Felt for their work on the information system.

Author information

Authors and Affiliations

  1. Center for Computational Regulatory Genomics, Beckman Institute, Caltech, Pasadena, CA, USA

    R. Andrew Cameron

Authors
  1. R. Andrew Cameron
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Editor information

Editors and Affiliations

  1. Florida Institute of Technology Dept. Biological Sciences, Melbourne, Florida, USA

    David J. Carroll

  2. University of New Mexico Dept. Biology, Albuquerque, New Mexico, USA

    Stephen A. Stricker

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© 2014 Springer Science+Business Media, New York

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Cameron, R.A. (2014). Tools for Sea Urchin Genomic Analysis. In: Carroll, D., Stricker, S. (eds) Developmental Biology of the Sea Urchin and Other Marine Invertebrates. Methods in Molecular Biology, vol 1128. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-974-1_20

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  • DOI: https://doi.org/10.1007/978-1-62703-974-1_20

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-973-4

  • Online ISBN: 978-1-62703-974-1

  • eBook Packages: Springer Protocols

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