The UCSC SARS-CoV-2 Genome Browser.
The UCSC SARS-CoV-2 Genome Browser.
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DOI：
10.1038/s41588-020-0700-8
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发表时间：
2020-10
期刊：
影响因子：
30.8
通讯作者：
Haeussler M
中科院分区：
文献类型：
--
作者：
Fernandes JD;Hinrichs AS;Clawson H;Gonzalez JN;Lee BT;Nassar LR;Raney BJ;Rosenbloom KR;Nerli S;Rao AA;Schmelter D;Fyfe A;Maulding N;Zweig AS;Lowe TM;Ares M Jr;Corbet-Detig R;Kent WJ;Haussler D;Haeussler M
在COVID-19大流行期间，研究人员正在以前所未有的速度生成与SARS-CoV-2 RNA基因组及其蛋白质有关的分子数据。因此，迫切需要以一种格式快速和持续更新地访问最新的分子数据，以便所有数据可以快速交叉引用和比较。为此，我们将我们的基因组浏览器可视化工具调整为病毒基因组。从已发表的研究或数据库提交中整理出来的分子数据被映射到病毒基因组中，并分组到“注释轨道”中，在那里它们可以沿着病毒基因组序列的线性图可视化，并以标准格式编程下载以供分析。UCSC SARS-CoV-2基因组浏览器（https://genome.ucsc.edu/covid19.html）提供了对储存在GISAID和国际核苷酸测序数据库中的数千个SARS-CoV-2基因组突变的持续更新访问，并与系统发育树一起显示。通过对蝙蝠、穿山甲以及其他动物和人类冠状病毒基因组的比对，包括对每个碱基的进化速率分析，增强了这些数据。所有可用的注释都在病毒基因组上交叉引用，包括来自主要数据库（PDB、RFAM、IEDB、UniProt）的注释以及来自预印本的最新单个结果。注释的数据包括预测和验证的免疫表位、有希望的抗体、RT-PCR和测序引物、CRISPR指南（来自研究、诊断、疫苗和治疗）以及人类和病毒基因之间的相互作用点。作为一个社区资源，任何用户都可以添加手工注释，这些注释经过质量检查，并在第二天在浏览器上公开共享。我们邀请所有研究人员为该资源提供额外的数据和注释，以加速全球的研究和开发活动。请与我们联系genome-www@soe.ucsc.edu，提供数据建议或请求支持添加数据。数据的快速共享将加速SARS-CoV-2的研究，特别是当研究人员花时间将他们的数据与其他实验室的数据整合到一个广泛使用的社区浏览器平台上，该平台具有标准化的机器可读数据格式，如SARS-CoV-2基因组浏览器。
Researchers are generating molecular data pertaining to the SARS-CoV-2 RNA genome and its proteins at an unprecedented rate during the COVID-19 pandemic. As a result, there is a critical need for rapid and continuously updated access to the latest molecular data in a format in which all data can be quickly cross-referenced and compared. We adapted our genome browser visualization tool to the viral genome for this purpose. Molecular data, curated from published studies or from database submissions, are mapped to the viral genome and grouped together into “annotation tracks” where they can be visualized along the linear map of the viral genome sequence and programmatically downloaded in standard format for analysis. The UCSC Genome Browser for SARS-CoV-2 (https://genome.ucsc.edu/covid19.html) provides continuously updated access to the mutations in the many thousands of SARS-CoV-2 genomes deposited in GISAID and the international nucleotide sequencing databases, displayed alongside phylogenetic trees. These data are augmented with alignments of bat, pangolin, and other animal and human coronavirus genomes, including per-base evolutionary rate analysis. All available annotations are cross-referenced on the virus genome, including those from major databases (PDB, RFAM, IEDB, UniProt) as well as up-to-date individual results from preprints. Annotated data include predicted and validated immune epitopes, promising antibodies, RT-PCR and sequencing primers, CRISPR guides (from research, diagnostics, vaccines, and therapies), and points of interaction between human and viral genes. As a community resource, any user can add manual annotations which are quality checked and shared publicly on the browser the next day. We invite all investigators to contribute additional data and annotations to this resource to accelerate research and development activities globally. Contact us at genome-www@soe.ucsc.edu with data suggestions or requests for support for adding data. Rapid sharing of data will accelerate SARS-CoV-2 research, especially when researchers take time to integrate their data with those from other labs on a widely-used community browser platform with standardized machine-readable data formats, such as the SARS-CoV-2 Genome Browser.
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影响因子：
12.3
作者：
Buels R;Yao E;Diesh CM;Hayes RD;Munoz-Torres M;Helt G;Goodstein DM;Elsik CG;Lewis SE;Stein L;Holmes IH
通讯作者：
Holmes IH
影响因子：
--
作者：
Nakagawa K;Lokugamage KG;Makino S
通讯作者：
Makino S
影响因子：
3
作者：
Pettersen, EF;Goddard, TD;Ferrin, TE
通讯作者：
Ferrin, TE
影响因子：
12.3
作者：
Davidson, Andrew D.;Williamson, Maia Kavanagh;Matthews, David A.
通讯作者：
Matthews, David A.
影响因子：
64.5
作者：
Abbott, Timothy R.;Dhamdhere, Girija;Qi, Lei S.
通讯作者：
Qi, Lei S.