PseudoBase: a genomic visualization and exploration resource for the Drosophila pseudoobscura subgroup
PseudoBase: a genomic visualization and exploration resource for the Drosophila pseudoobscura subgroup
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DOI：
10.1080/19336934.2020.1864201
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发表时间：
2020-12
期刊：
影响因子：
1.2
通讯作者：
Katharine L Korunes;Russell B. Myers;Ryan Hardy;M. Noor
中科院分区：
文献类型：
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作者：
Katharine L Korunes;Russell B. Myers;Ryan Hardy;M. Noor
摘要果蝇是进化遗传学和基因组学研究的经典模式系统。鉴于这一长期的兴趣，许多基因组序列已经积累了假黑线刺蛾和与之密切相关的物种平纹夜蛾、米兰达和洛威的基因组序列。为了便于探索物种内的遗传变异和跨物种的比较基因组学，我们提出了PseudoBase，这是一个数据库，通过直观的图形界面将广泛的公开可用基因组数据与简单的可视化和查询工具结合在一起，可用于研究和教育环境。数据库中的所有遗传变异(SNPs和Indels)都来自相同的工作流程，因此变异很容易在数据集上进行比较。这些功能包括嵌入式jBrowser界面、提取单个基因/区域的比对以及批量访问基因列表的能力。在这里，我们介绍了假碱基，并演示了该资源如何促进使用大量的果蝇基因组数据的拟黑果蝇亚群。
ABSTRACT Drosophila pseudoobscura is a classic model system for the study of evolutionary genetics and genomics. Given this long-standing interest, many genome sequences have accumulated for D. pseudoobscura and closely related species D. persimilis, D. miranda, and D. lowei. To facilitate the exploration of genetic variation within species and comparative genomics across species, we present PseudoBase, a database that couples extensive publicly available genomic data with simple visualization and query tools via an intuitive graphical interface, amenable for use in both research and educational settings. All genetic variation (SNPs and indels) within the database is derived from the same workflow, so variants are easily comparable across data sets. Features include an embedded JBrowse interface, ability to pull out alignments of individual genes/regions, and batch access for gene lists. Here, we introduce PseudoBase, and we demonstrate how this resource facilitates use of extensive genomic data from flies of the Drosophila pseudoobscura subgroup.