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Nucleic Acids Res. 2015 Jan;43(Database issue):D756-63. doi: 10.1093/nar/gku956. Epub 2014 Oct 13.

Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes.

Author information

1
University of Calgary-Computer Science, Calgary, Alberta, Canada.
2
Cincinnati Children's Research Foundation-Division of Developmental Biology, Cincinnati, OH, USA.
3
University of Calgary-Computer Science, Calgary, Alberta, Canada University of Calgary-Biological Sciences, Calgary, Alberta, Canada pvize@ucalgary.ca.

Abstract

Xenbase (http://www.xenbase.org), the Xenopus frog model organism database, integrates a wide variety of data from this biomedical model genus. Two closely related species are represented: the allotetraploid Xenopus laevis that is widely used for microinjection and tissue explant-based protocols, and the diploid Xenopus tropicalis which is used for genetics and gene targeting. The two species are extremely similar and protocols, reagents and results from each species are often interchangeable. Xenbase imports, indexes, curates and manages data from both species; all of which are mapped via unique IDs and can be queried in either a species-specific or species agnostic manner. All our services have now migrated to a private cloud to achieve better performance and reliability. We have added new content, including providing full support for morpholino reagents, used to inhibit mRNA translation or splicing and binding to regulatory microRNAs. New genomes assembled by the JGI for both species and are displayed in Gbrowse and are also available for searches using BLAST. Researchers can easily navigate from genome content to gene page reports, literature, experimental reagents and many other features using hyperlinks. Xenbase has also greatly expanded image content for figures published in papers describing Xenopus research via PubMedCentral.

PMID:
25313157
PMCID:
PMC4384024
DOI:
10.1093/nar/gku956
[Indexed for MEDLINE]
Free PMC Article

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