SilkDB 3.0: visualizing and exploring multiple levels of data for silkworm
SilkDB 3.0: visualizing and exploring multiple levels of data for silkworm
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SilkDB 3.0：可视化和探索蚕的多层次数据
DOI：
10.1093/nar/gkz919
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发表时间：
2020-01-08
影响因子：
14.9
通讯作者：
Wang, Yi
中科院分区：
文献类型：
--
作者：
Lu, Fang;Wei, Zhaoyuan;Wang, Yi
SilkDB是一个开放访问的数据库和强大的平台，提供有关家蚕基因组的全面信息。自10年前SilkDB 2.0发布以来，已经产生了关于家蚕多个方面的大量数据，包括基因组，转录组，Hi-C和泛基因组。为了在这些不同的生物水平上可视化数据，我们提出了SilkDB 3.0（https：silkdb.bioinfotoolkits.net），这是一个通过交互式用户界面探索家蚕数据的可视化分析工具。该数据库包含高质量的家蚕基因组染色体水平组装，其编码序列和基因组比以前的版本更准确。SilkDB 3.0提供了每个基因在序列、蛋白质结构、基因家族、同源性、同线性、基因组组织水平上的信息视图，并提供了对基因表达信息、遗传变异和基因组相互作用图谱的访问。一组可视化工具可用于显示上述数据集中的丰富信息。通过改进的交互式用户界面来整合大型数据集，更新后的SilkDB 3.0数据库将成为蚕和昆虫研究界的宝贵资源。
SilkDB is an open-accessibility database and powerful platform that provides comprehensive information on the silkworm (Bombyx mori) genome. Since SilkDB 2.0 was released 10 years ago, vast quantities of data about multiple aspects of the silkworm have been generated, including genome, transcriptome, Hi-C and pangenome. To visualize data at these different biological levels, we present SilkDB 3.0 (https://silkdb.bioinfotoolkits.net), a visual analytic tool for exploring silkworm data through an interactive user interface. The database contains a high-quality chromosome-level assembly of the silkworm genome, and its coding sequences and gene sets are more accurate than those in the previous version. SilkDB 3.0 provides a view of the information for each gene at the levels of sequence, protein structure, gene family, orthology, synteny, genome organization and gives access to gene expression information, genetic variation and genome interaction map. A set of visualization tools are available to display the abundant information in the above datasets. With an improved interactive user interface for the integration of large data sets, the updated SilkDB 3.0 database will be a valuable resource for the silkworm and insect research community.