Web-based visualization of coronavirus genomes and proteins

项目摘要 这一补充建议将几个生物信息学 SARS-CoV-2基因组分析服务中的可视化工具。 该提案的核心是一个新的原型JavaScript查看器， ABrowse，能够呈现多个序列比对， 可通过系统发育树导航，并与蛋白质结构整合 视图，所有这些都在一个可嵌入的组件中。ABrowse查看器是 目前用于提供Pfam SARS-CoV-2特别版本： 冠状病毒基因组的40个蛋白质结构域的集合，沿着 PDB结构。（ABrowse也是Pfam未来的候选人 默认查看器，如支持信函中所述。） 我们建议加速ABrowse的开发， COVID-19大流行，专门针对扩展、性能和 科学家研究的最相关的一体化问题， 病毒其中最主要的是扩展ABrowse以处理数百万个 蛋白质序列（和/或SARS-CoV-2基因组序列）， 一种新的压缩存储格式，适用于 随机访问用户驱动的探索非常大的树（和 对齐）。 除了可扩展性，我们还解决了集成问题，为 ABrowse在JBrowse（基因组浏览器， 本项目的补充建议书）以及 Auspice（NextStrain的网络仪表板，系统发育基因组 广泛用于COVID-19的对齐和注释包 分析）。我们还提出了几个用户界面增强， 使ABrowse作为COVID-19数据的导航工具更加有用。

Project Summary This supplemental proposal knits together several bioinformatics visualization tools in the service of SARS-CoV-2 genome analysis. The core of the proposal is a newly-prototyped JavaScript viewer, ABrowse, that is capable of rendering multiple sequence alignments, navigable by phylogenetic trees, and integrated with protein structure views, all in a single embeddable component. The ABrowse viewer is currently employed to render the Pfam SARS-CoV-2 special release: a collection of 40 protein domains from the coronavirus genome, along with PDB structures. (ABrowse is also a candidate for Pfam's future default viewer, as noted in the letters of support.) We propose to accelerate ABrowse development for use by the COVID-19 pandemic, specifically targeting scaling, performance, and integration issues that are most relevant to scientists studying the virus. Chief amongst these is scaling ABrowse to handle millions of protein sequences (and/or SARS-CoV-2 genome sequences) by means of a new, compressed storage format suitable for random-access user-driven exploration of very large trees (and alignments) over the web. Beyond scaling, we also address integration, developing plugins for ABrowse to run within JBrowse (the genome browser that is the focus of the project to which this is a supplemental proposal) as well as Auspice (the web dashboard of NextStrain, the phylogenetic genome alignment and annotation package that is widely used for COVID-19 analysis). We also propose several user interface enhancements to make ABrowse more useful as a navigation tool for COVID-19 data.