Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA.
Nucleic Acids Res. 2019 Jan 8;47(D1):D678-D686. doi: 10.1093/nar/gky1127.
The Integrated Microbial Genome/Virus (IMG/VR) system v.2.0 (https://img.jgi.doe.gov/vr/) is the largest publicly available data management and analysis platform dedicated to viral genomics. Since the last report published in the 2016, NAR Database Issue, the data has tripled in size and currently contains genomes of 8389 cultivated reference viruses, 12 498 previously published curated prophages derived from cultivated microbial isolates, and 735 112 viral genomic fragments computationally predicted from assembled shotgun metagenomes. Nearly 60% of the viral genomes and genome fragments are clustered into 110 384 viral Operational Taxonomic Units (vOTUs) with two or more members. To improve data quality and predictions of host specificity, IMG/VR v.2.0 now separates prokaryotic and eukaryotic viruses, utilizes known prophage sequences to improve taxonomic assignments, and provides viral genome quality scores based on the estimated genome completeness. New features also include enhanced BLAST search capabilities for external queries. Finally, geographic map visualization to locate user-selected viral genomes or genome fragments has been implemented and download options have been extended. All of these features make IMG/VR v.2.0 a key resource for the study of viruses.
IMG/VR 系统 v.2.0（https://img.jgi.doe.gov/vr/）是目前最大的公共病毒基因组学数据管理和分析平台。自 2016 年 NAR 数据库增刊发表上一次报告以来，数据量增加了两倍，目前包含了 8389 个已培养参考病毒的基因组、12498 个源自已培养微生物分离物的以前发表的经精心整理的噬菌体，以及从组装的宏基因组中计算预测的 735112 个病毒基因组片段。近 60%的病毒基因组和基因组片段聚类为 110384 个具有两个或更多成员的病毒操作分类单元 (vOTU)。为了提高数据质量和宿主特异性预测，IMG/VR v.2.0 现在将原核和真核病毒分开，利用已知的噬菌体序列来改进分类分配，并根据估计的基因组完整性提供病毒基因组质量评分。新功能还包括增强了用于外部查询的 BLAST 搜索功能。最后，实现了用户选择的病毒基因组或基因组片段的地理图谱可视化，并扩展了下载选项。所有这些功能使 IMG/VR v.2.0 成为病毒研究的重要资源。
