Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes.
Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes.
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DOI：
10.1093/nar/gku956
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发表时间：
2015-01
影响因子：
14.9
通讯作者：
Vize PD
中科院分区：
文献类型：
--
作者：
Karpinka JB;Fortriede JD;Burns KA;James-Zorn C;Ponferrada VG;Lee J;Karimi K;Zorn AM;Vize PD
XenBASE(http://www.xenbase.org)，)非洲爪蛙模式生物体数据库，集成了来自该生物医学模式属的各种数据。代表了两个密切相关的物种：被广泛用于显微注射和组织外植体程序的异源四倍体非洲爪哇，以及用于遗传学和基因靶向的二倍体热带非洲爪哇。这两个物种极其相似，每个物种的方案、试剂和结果往往是可以互换的。Xenbase从这两个物种导入、索引、管理和管理数据；所有这些数据都通过唯一的ID进行映射，并且可以以特定于物种或与物种无关的方式进行查询。我们的所有服务现在都已迁移到私有云，以实现更好的性能和可靠性。我们增加了新的内容，包括为用于抑制mRNA翻译或剪接和与调节microRNAs结合的吗啡诺试剂提供完全支持。JGI为这两个物种组装了新的基因组，并在GBROWSE中显示，也可以使用BLAST进行搜索。研究人员可以使用超链接轻松地从基因组内容导航到基因页面报告、文献、实验试剂和许多其他功能。Xenbase还通过PubMedCentral大大扩展了描述Xenopus研究的论文中发表的人物的图像内容。
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.
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