Web-based visualization of coronavirus genomes and proteins

基于网络的冠状病毒基因组和蛋白质可视化

• 批准号: 10162044
• 负责人: Ian H Holmes
• 金额: $ 35.48万
• 依托单位: UNIVERSITY OF CALIFORNIA BERKELEY
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-04 至 2021-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10162044
• 关键词: 2019-nCoV; Address; Algorithms; Amino Acid Sequence; Amino Acids; Antiviral Agents; Bioinformatics; COVID-19; COVID-19 pandemic; Collection; Coronavirus; Data; Data Set; Databases; Development; Engineering; Epidemiology; Future; Genome; Genomics; Home environment; Individual; Internet; Length; Letters; Mus; Online Systems; Performance; Phylogenetic Analysis; Phylogeny; Proteins; Research Personnel; Resources; Running; Scientist; Sequence Alignment; Services; Shelter facility; Software Tools; Structure; Tertiary Protein Structure; Time; Trees; Update; Vaccines; Variant; Viral; Virus; Visualization; Visualization software; base; bioinformatics tool; cloud storage; dashboard; genetic variant; genome analysis; genome annotation; genome browser; indexing; innovation; interest; interoperability; pathogen; protein structure; prototype; reconstruction; response; tool; web app

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.

项目摘要 这个补充提案编织在一起几种生物信息学 SARS-COV-2基因组分析服务中的可视化工具。 该提案的核心是新推销的JavaScript查看器， 简化，能够呈现多个序列比对， 可通过系统发育树航行，并与蛋白质结构集成 视图，全部都在一个可嵌入的组件中。简化的查看器是 目前被用来渲染PFAM SARS-COV-2特别版本： 沿着冠状病毒基因组的40个蛋白质结构域的集合 与PDB结构。 （Abrowse也是PFAM未来的候选人 默认查看器，如支持信中所述。 我们建议加速逐步发展开发 COVID-19大流行，专门针对缩放，性能和 与研究的科学家最相关的整合问题 病毒。其中最主要的是扩大缩减以处理数百万 蛋白质序列（和/或SARS-COV-2基因组序列）通过 一种新的压缩存储格式的方式 随机访问用户驱动的非常大的树木（和 对齐）在网上。 除了扩展外，我们还解决集成，开发插件 在JBrowse（基因组浏览器是焦点）中逐渐运行 这是一个补充建议的项目） Auspice（Nextstrain的Web仪表板，系统发育基因组 对齐和注释包广泛用于COVID-19 分析）。我们还建议了几个用户界面增强功能 使其作为COVID-19数据的导航工具更有用。