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Integration of 1:1 orthology maps and updated datasets into Echinobase.

Authors :
Foley, Saoirse
Ku, Carolyn
Arshinoff, Brad
Lotay, Vaneet
Karimi, Kamran
Vize, Peter D
Hinman, Veronica
Source :
Database: The Journal of Biological Databases & Curation. 2021, Vol. 2021, p1-7. 7p.
Publication Year :
2021

Abstract

Echinobase (https://echinobase.org) is a central online platform that generates, manages and hosts genomic data relevant to echinoderm research. While the resource primarily serves the echinoderm research community, the recent release of an excellent quality genome for the frequently studied purple sea urchin (Strongylocentrotus purpuratus genome, v5.0) has provided an opportunity to adapt to the needs of a broader research community across other model systems. To this end, establishing pipelines to identify orthologous genes between echinoderms and other species has become a priority in many contexts including nomenclature, linking to data in other model organisms, and in internal functionality where data gathered in one hosted species can be associated with genes in other hosted echinoderms. This paper describes the orthology pipelines currently employed by Echinobase and how orthology data are processed to yield 1:1 ortholog mappings between a variety of echinoderms and other model taxa. We also describe functions of interest that have recently been included on the resource, including an updated developmental time course for S. purpuratus , and additional tracks for genome browsing. These data enhancements will increase the accessibility of the resource to non-echinoderm researchers and simultaneously expand the data quality and quantity available to core Echinobase users. Database URL : https://echinobase.org [ABSTRACT FROM AUTHOR]

Details

Language :
English
ISSN :
17580463
Volume :
2021
Database :
Academic Search Index
Journal :
Database: The Journal of Biological Databases & Curation
Publication Type :
Academic Journal
Accession number :
155028449
Full Text :
https://doi.org/10.1093/database/baab030