As the global health emergency around the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, formerly 2019-nCoV, Wuhan coronavirus) continues, we continue to play a key role in providing the biomedical community free and easy access to genome sequences from the coronavirus. You can quickly access these data through the NCBI search (Figure 1).
When there is an outbreak of dengue fever in the world, it’s critical that viral genomic sequence data be submitted by researchers and made available to analyze as soon as possible. You can now submit Dengue virus sequences to GenBank using a new workflow (Figure 1) in the Submission Portal designed to help make these data available as soon as possible. The streamlined process, similar to the one described in a previous post for animal mitochondrial COX1 sequences, has an improved interface, enhanced validation, and automatic annotation that saves you time and effort.
Figure 1. The Submission Portal pages for targeted sequence submission workflows. Top panel. The new submission page for entering the workflow. Bottom panel. Submission Portal page with the Dengue virus submission option selected (boxed in red). The service has options for other targeted submissions including mitochondrial COX1 from multicellular animals (metazoa), ribosomal RNA (rRNA), rRNA-ITS, Influenza virus, and Norovirus sequences.
This update is part of a larger and ongoing effort to consolidate GenBank submissions in a central location. In addition to Dengue virus data, you can also submit Influenza A, B, C and Norovirus sequences as well as other targeted sequences including mitochondrial COX1 genes from multicellular animals (metazoa), ribosomal RNA (rRNA), and rRNA-ITS through the options on the Submission Portal. You should submit other types of sequence data including other virus sequences to GenBank using BankIt or tbl2ASN.
You can use the search feature on the Submission Portal to find the appropriate submission tool for your data.
Get rapid access to Wuhan coronavirus (2019-nCoV) sequence data from the current outbreak as it becomes available. We will continue to update the page with newly released data.
The complete annotated genome sequence of the novel coronavirus associated with the outbreak of pneumonia in Wuhan, China is now available from GenBank for free and easy access by the global biomedical community. Figure 1 shows the relationship of the Wuhan virus to selected coronaviruses.
Figure 1. Phylogenetic tree showing the relationship of Wuhan-Hu-1 (circled in red) to selected coronaviruses. Nucleotide alignment was done with MUSCLE 3.8. The phylogenetic tree was estimated with MrBayes 3.2.6 with parameters for GTR+g+i. The scale bar indicates estimated substitutions per site, and all branch support values are 99.3% or higher.
We are pleased to announce the second installment of the Virus Hunting Codeathon that will take place from November 4-6, 2019 at the University of Maryland in College Park.
The NCBI will help run this bioinformatics codeathon, hosted by the UMIACS and CBCB at the University of Maryland. The purpose of this event is to continue develop techniques, code, and pipelines to identify known, taxonomically definable, and novel viruses from metagenomic datasets on cloud infrastructure.
This event is for researchers, including students and postdocs, who are already engaged in the use of bioinformatics data or in the development of pipelines for virological analyses from high-throughput experiments. We especially encourage people who have experience in Computational Virus Hunting or related fields to participate. The event is open to anyone selected for the codeathon and willing to travel to College Park (see below).
TOPICS
Fast, federated indexing
Big Query
Metadata features
Genome graphs for viruses
Approximate taxonomic analysis
Domain/HMM Boundary and Taxonomic Refinement
Bringing together approximate taxonomy and domain models
Sequence data quality metrics
Phage-host interactions
We will provide the final list of projects before the codeathon starts.
If you are, join us in a few days for a workshop on the virus hunting hackathon we helped run earlier this year.
Session: Workshop #19: Virus Discovery
Program Number: W-19-8
Time: Sunday, July 21, 7:00 PM CDT
Location: Mayo Auditorium
In this workshop, Dr. Rodney Brister will talk about how 41 scientists from 21 organizations worked to improve the usability of SRA data, identifying datasets that included known viruses and viral signals. Not only is that information now being integrated into a public search interface, but the approach used is also being refined in future hackathons so it can be applied to all SRA datasets.
We have a new and improved search experience for viral genes from select human pathogens. When you search for a virus such as HIV-1 (more examples below), you now get an interactive graphical representation of the viral genome where you can see all the annotated viral proteins in context. Clicking on the gene / protein objects allows you to access sequences, publications, and analysis tools for the selected protein. This new feature is designed to help you quickly find information relevant to your research on clinically important viruses.Figure 1. Top: The virus genome graphic result for a search with HIV-1 with access to analysis tools, downloads, and relevant results in the Genome and Virus resources. Bottom: The result obtained by clicking the env gene graphic, which provides links to protein and nucleotide sequences, the literature, analysis tools, and downloads.
Try it out using the following example searches and let us know what you think!
Do you have Norovirus sequence data to submit to GenBank? Try out the newly-released improvements in our submission service for Norovirus data! The new service offers the following advantages:
Faster processing and shorter time to accession numbers
Improved user interface
Automatic Feature annotation
Figure 1. The submission portal page showing the new option for submitting Norovirus data.
From January 9th – 11th, the NCBI will help run a bioinformatics hackathon in Southern California hosted by the Computational Sciences Research Center at San Diego State University. We reached out to the global computational biology and virology community as part of this effort to make data more accessible.
The hackathon teams look forward to leveraging metagenomic datasets in the cloud to find data based on organismal content and update taxonomy – but most of all – hunt down new viruses!
Follow along with the event with NCBI tweets and see our work on GitHub.
We’re specifically looking for folks who have experience in computational virus hunting or adjacent fields to identify known, taxonomically-definable and novel viruses from a few hundred thousand metagenomic datasets that we’ll put on cloud infrastructure. This event is for researchers, including students and postdocs, who are already engaged in the use of bioinformatics data or in the development of pipelines for virological analyses from high-throughput experiments. If this describes you, please apply! The event is open to anyone selected for the hackathon and willing to travel to SDSU (see below).
The 2018 Nucleic Acids Research database issue features several papers from NCBI staff that cover the status and future of databases including CCDS, ClinVar, GenBank and RefSeq. These papers are also available on PubMed. To read an article, click on the PMID number listed below.
Figure 1. NCBI search results for the term “wuhan coronavirus” showing the buttons that link to the data in the NCBI Virus resource, GenBank®/SRA , and a specialized BLAST page that searches Betacoronavirus sequences.
