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MpoxRadar:一个全球性的 MPXV 基因组监测仪表板。

MpoxRadar: a worldwide MPXV genomic surveillance dashboard.

机构信息

Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 Potsdam, Germany.

Genome Competence Center (MF1), Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany.

出版信息

Nucleic Acids Res. 2023 Jul 5;51(W1):W331-W337. doi: 10.1093/nar/gkad325.

Abstract

The mpox virus (MPXV) is mutating at an exceptional rate for a DNA virus and its global spread is concerning, making genomic surveillance a necessity. With MpoxRadar, we provide an interactive dashboard to track virus variants on mutation level worldwide. MpoxRadar allows users to select among different genomes as reference for comparison. The occurrence of mutation profiles based on the selected reference is indicated on an interactive world map that shows the respective geographic sampling site in customizable time ranges to easily follow the frequency or trend of defined mutations. Furthermore, the user can filter for specific mutations, genes, countries, genome types, and sequencing protocols and download the filtered data directly from MpoxRadar. On the server, we automatically download all MPXV genomes and metadata from the National Center for Biotechnology Information (NCBI) on a daily basis, align them to the different reference genomes, generate mutation profiles, which are stored and linked to the available metainformation in a database. This makes MpoxRadar a practical tool for the genomic survaillance of MPXV, supporting users with limited computational resources. MpoxRadar is open-source and freely accessible at https://MpoxRadar.net.

摘要

猴痘病毒(MPXV)的突变速度在 DNA 病毒中是异常的,其全球传播令人担忧,因此基因组监测是必要的。我们通过 MpoxRadar 提供了一个交互式仪表板,用于在全球范围内跟踪病毒变异的突变水平。MpoxRadar 允许用户在不同的基因组之间进行选择,作为比较的参考。根据所选参考的突变谱发生情况在交互式世界地图上进行指示,该地图显示了可自定义时间范围的相应地理采样地点,以便轻松跟踪定义突变的频率或趋势。此外,用户可以按特定的突变、基因、国家、基因组类型和测序方案进行筛选,并直接从 MpoxRadar 下载筛选后的数据。在服务器端,我们每天自动从国家生物技术信息中心 (NCBI) 下载所有 MPXV 基因组和元数据,将它们与不同的参考基因组进行比对,生成突变谱,并将其存储并与数据库中可用的元信息相关联。这使得 MpoxRadar 成为监测 MPXV 基因组的实用工具,为计算资源有限的用户提供支持。MpoxRadar 是开源的,并可在 https://MpoxRadar.net 上免费访问。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e0f0/10320163/c72243f8ee32/gkad325figgra1.jpg

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