Echinobase: an expanding resource for echinoderm genomic information
- Creators
- Kudtarkar, Parul
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Cameron, R. Andrew
Abstract
Echinobase, a web accessible information system of diverse genomics and biological data for the echinoderm clade, grew out of SpBase, the first echinoderm genome project for sea urchin, Strongylocentrotus purpuratus. Sea urchins and their relatives are utilitarian research models in fields ranging from marine biology to developmental biology and gene regulatory systems. Echinobase is a user-friendly web interface that links an array of biological data that would otherwise have been tedious and frustrating for researchers to extract and organize. The system hosts a powerful gene search engine, genomics browser and other bioinformatics tools to investigate genomics and high throughput data. The Echinobase information system now serves genomic information for eight echinoderm species: S. purpuratus, Strongylocentrotus fransciscanus, Allocentrotus fragilis, Lytechinus variegatus, Patiria miniata, Parastichopus parvimensis and Ophiothrix spiculata, Eucidaris tribuloides. Herein lies a description of the web information system, genomics data types and content hosted by Echinobase.org. The goal of Echinobase is to connect genomic information to various experimental data and accelerate the research in field of molecular biology, developmental process, gene regulatory networks and more recently engineering biological systems0. Database URL:http://www.echinobase.org
Additional Information
© 2017 The Author(s). Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Received 19 June 2017; Revised 4 August 2017; Accepted 23 August 2017. Published: 12 September 2017. We thank Ung-Jin Kim, Susan Gordon for their annotation work and David Felt for system administration work on the Echinobase website and the data therein. We are grateful to our colleagues and collaborators on Echinobase and Echinoderm sequencing project; Susan Ernst, Ann Cutting, Kari Koppitch, Lijun Wang, Kim Worley, Richard Gibbs, David Mathog, Greg Cary, and Veronica Hinman. We acknowledge late Professor Eric Davidson and members of the Davidson laboratory for sharing sequence and experimental data. Dr Greg Cary kindly reviewed the manuscript and made thoughtful suggestions. This work was supported by Eunice Kennedy Shriver National Institute of Child Health and Human Development at National Institutes of Health (P41HD071837 to R.A.C.) and by the Beckman Institute at California Institute of Technology. Conflict of interest. None declared.Attached Files
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Additional details
- Eprint ID
- 82538
- Resolver ID
- CaltechAUTHORS:20171020-130016276
- P41HD071837
- NIH
- Caltech Beckman Institute
- Created
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2017-10-20Created from EPrint's datestamp field
- Updated
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2021-11-15Created from EPrint's last_modified field