PseudoBase: a genomic visualization and exploration resource for the Drosophila pseudoobscura subgroup.

IF 2.4 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Fly Pub Date : 2021-12-01 DOI:10.1080/19336934.2020.1864201

Katharine L Korunes, Russell B Myers, Ryan Hardy, Mohamed A F Noor

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引用次数: 0

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.

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PseudoBase：假褐腹果蝇亚群的基因组可视化和探索资源。

假鳞翅目果蝇是研究进化遗传学和基因组学的经典模式系统。鉴于这种长期存在的兴趣，我们已经积累了许多伪胸腺果蝇和密切相关物种 D. persimilis、D. miranda 和 D. lowei 的基因组序列。为了便于探索物种内的遗传变异和物种间的比较基因组学，我们推出了 PseudoBase 数据库，该数据库通过直观的图形界面将大量公开的基因组数据与简单的可视化和查询工具结合在一起，适合在研究和教育环境中使用。数据库中的所有基因变异（SNPs 和 indels）都来自相同的工作流程，因此不同数据集之间的变异很容易进行比较。该数据库的功能包括嵌入式 JBrowse 界面、提取单个基因/区域的比对结果以及批量访问基因列表。在这里，我们将介绍 PseudoBase，并演示该资源如何帮助使用来自假鳞翅目果蝇亚群的大量基因组数据。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Fly 生物-生化与分子生物学

CiteScore

2.90

自引率

0.00%

发文量

审稿时长

>12 weeks

期刊介绍： Fly is the first international peer-reviewed journal to focus on Drosophila research. Fly covers a broad range of biological sub-disciplines, ranging from developmental biology and organogenesis to sensory neurobiology, circadian rhythm and learning and memory, to sex determination, evolutionary biology and speciation. We strive to become the “to go” resource for every researcher working with Drosophila by providing a forum where the specific interests of the Drosophila community can be discussed. With the advance of molecular technologies that enable researchers to manipulate genes and their functions in many other organisms, Fly is now also publishing papers that use other insect model systems used to investigate important biological questions. Fly offers a variety of papers, including Original Research Articles, Methods and Technical Advances, Brief Communications, Reviews and Meeting Reports. In addition, Fly also features two unconventional types of contributions, Counterpoints and Extra View articles. Counterpoints are opinion pieces that critically discuss controversial papers questioning current paradigms, whether justified or not. Extra View articles, which generally are solicited by Fly editors, provide authors of important forthcoming papers published elsewhere an opportunity to expand on their original findings and discuss the broader impact of their discovery. Extra View authors are strongly encouraged to complement their published observations with additional data not included in the original paper or acquired subsequently.