Enhancing the GABI-Kat Arabidopsis thaliana T-DNA Insertion Mutant Database by Incorporating Araport11 Annotation.
Enhancing the GABI-Kat Arabidopsis thaliana T-DNA Insertion Mutant Database by Incorporating Araport11 Annotation.
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DOI：
10.1093/pcp/pcw205
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发表时间：
2017-01-01
影响因子：
4.9
通讯作者：
Weisshaar B
中科院分区：
文献类型：
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作者：
Kleinboelting N;Huep G;Weisshaar B
SimpleSearch提供对数据库的访问，该数据库包含关于拟南芥突变体Gabi-Kat集合的T-DNA插入线的信息。这些突变体是反向遗传学的重要工具，Gabi-Kat是此类T-DNA插入突变体的第二大集合。插入位点是从侧翼序列标签(FST)推断出来的，数据库包含有关突变植物品系和插入等位基因的信息。在这里，我们描述了界面内的改进(可在http://www.gabi-kat.de/db/genehits.php)获得)，以及在过去五年中实现的数据库内容。这些改进包括集成了Araport11基因组序列注释数据，该数据包含最近更新的A.thaliana结构基因描述，更新的可视化组件显示具有非常相似的插入位置、映射的确认序列和引物的插入物组。可视化组件提供了一种快速识别感兴趣的插入的方法，并访问关于确认的插入等位基因的确切结构的改进数据。此外，通过纳入在确认过程中检测到的其他插入等位基因，以及通过增加在继续努力弥补FST可用性差距期间产生的新的FST，扩展了数据库的内容。最后，关于预测和确认的插入等位基因以及引物序列的当前数据库内容已经以可下载的平面文件的形式提供。
SimpleSearch provides access to a database containing information about T-DNA insertion lines of the GABI-Kat collection of Arabidopsis thaliana mutants. These mutants are an important tool for reverse genetics, and GABI-Kat is the second largest collection of such T-DNA insertion mutants. Insertion sites were deduced from flanking sequence tags (FSTs), and the database contains information about mutant plant lines as well as insertion alleles. Here, we describe improvements within the interface (available at http://www.gabi-kat.de/db/genehits.php) and with regard to the database content that have been realized in the last five years. These improvements include the integration of the Araport11 genome sequence annotation data containing the recently updated A. thaliana structural gene descriptions, an updated visualization component that displays groups of insertions with very similar insertion positions, mapped confirmation sequences, and primers. The visualization component provides a quick way to identify insertions of interest, and access to improved data about the exact structure of confirmed insertion alleles. In addition, the database content has been extended by incorporating additional insertion alleles that were detected during the confirmation process, as well as by adding new FSTs that have been produced during continued efforts to complement gaps in FST availability. Finally, the current database content regarding predicted and confirmed insertion alleles as well as primer sequences has been made available as downloadable flat files.