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

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.

SUBMITTER: Foley S

PROVIDER: S-EPMC8132956 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature

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

Foley Saoirse S Ku Carolyn C Arshinoff Brad B Lotay Vaneet V Karimi Kamran K Vize Peter D PD Hinman Veronica V

Database : the journal of biological databases and curation 20210501

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 pipeline ...[more]

PMID: 34010390

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

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

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