The World Health Organization (WHO) declared the recent upsurge of the mpox virus to be a public health emergency of international concern. Having timely viral genome data freely and widely available enables researchers to explore how this virus differs from viruses isolated and sequenced in the past. Therefore, NCBI’s GenBank is expediting the release of mpox data by annotating gene and coding region features as part of the submission process. Continue reading “Quick & Easy Access to Mpox Data Through NCBI Virus”
Tag: NCBI Virus
Coming Soon! Rapid Access to Influenza Data
Improved Influenza GenBank submission process
Do you submit flu sequences to GenBank? Thanks to community feedback, NCBI is excited to announce that we are improving the influenza GenBank submission process. We continue to play a key role in providing the biomedical community free and easy access to genome sequences from viruses. To further advance public health research, in the coming weeks we will begin to expedite the release of influenza data. This means you will see the rapid assignment of accession numbers and data becoming publicly accessible within hours. In addition, we will automatically process all Influenza genomes to produce standardized, consistent annotation which saves you time and benefits the researchers who find your data valuable. Continue reading “Coming Soon! Rapid Access to Influenza Data”
Now Available: Assembled Genomes for Influenza Viruses and Improved Functionality of NCBI Virus
NCBI Virus now offers genomes for viruses such as Influenza A by using an automated process to group segments from the same samples. We group these segments into genomes based on metadata for the sample including species, isolate name, host organism, collection date, and location. Newly released GenBank records are added daily.
Access these genome assemblies through NCBI Virus using the new “NCBI Virus Assembly” tab above the Results Table as shown below. Continue reading “Now Available: Assembled Genomes for Influenza Viruses and Improved Functionality of NCBI Virus”
New Data Available! Access Avian Influenza A (H5N1) Virus Sequences at NCBI
Sequence data from the ongoing avian influenza A (H5N1) virus outbreak in cattle are now available through NLM’s NCBI resources NCBI Virus and NCBI Datasets.
These data were submitted by the U.S. Department of Agriculture (USDA), U.S. Centers for Disease Control and Prevention (CDC), the World Health Organization (WHO), Iowa State University, and St. Jude Children’s Research Hospital. Continue reading “New Data Available! Access Avian Influenza A (H5N1) Virus Sequences at NCBI”
Upcoming Changes to Virus Data Resources at NCBI
Effective June 2024, NCBI Virus will replace legacy virus web resources
Coming soon! As part of our ongoing effort to enhance your experience and modernize our services, several of our legacy virus-related web resources will be replaced by NCBI Virus – our community portal for viral sequence data. NCBI Virus is more comprehensive, modernized, and has more powerful features and analysis tools than our legacy resources.
What will change?
Below is a list of the legacy virus resources that will be replaced by NCBI Virus. The list includes a description of features that will continue to be supported through NCBI Virus: Continue reading “Upcoming Changes to Virus Data Resources at NCBI”
NCBI Virus: Mutation-Based Search for SARS-CoV-2 Data
Millions of SARS-CoV-2 samples from around the world have been made publicly available as assembled and unassembled sequence data in GenBank and the Sequence Read Archive (SRA). Now you can find sequences with a particular mutation by searching with the protein and the amino acid change (e.g. S:F486V). Visit our SARS-CoV-2 Variant Overview on NCBI Virus and click on the ‘Mutation’ tab to get started (Figure 1).
Figure 1: SARS-CoV-2 Variants Overview. Arrows indicate important features on the page, including the “Lineages” and “Mutations” tabs to switch between views, the search box, and the information box describing the mutation format. The results are also indicated, including a summary of the total records found that contain the searched term as well as the results table. Continue reading “NCBI Virus: Mutation-Based Search for SARS-CoV-2 Data”
NCBI SARS-CoV-2 Resources Page Will Redirect Soon
End of the COVID-19 Public Health Emergency
During the COVID-19 pandemic, we provided the NCBI SARS-CoV-2 Resources Page as a central location to help you quickly and easily find our SARS-CoV-2 related content and tools. Since the federal public health emergency is now over, this page will be redirected to the SARS-CoV-2 Data Hub in NCBI Virus effective August 1, 2023.
Don’t worry! All this information will remain available. Check out the NLM Knowledge Base to access a list of NCBI SARS-CoV-2 data and tools.
Stay up to date
Follow us on Twitter @NCBI and join our mailing list to keep up to date with NCBI Virus and other NCBI news.
Questions?
If you have questions or would like to provide feedback, please reach out to us at info@ncbi.nlm.nih.gov.
Download Randomized Data Subset from NCBI Virus
Do you need a smaller dataset for your analyses of virus data? In response to your feedback, NCBI Virus now allows you to download a randomized subset of your results for nucleotide, protein, or RefSeq genome sequences from any supported virus (Figure 1). This option is useful for viruses such as SARS-CoV-2 or Influenza A that have very large numbers of records, where the entire dataset may present a challenge. In such cases, a smaller representative sample is easier to work with to support your analysis. You can also reduce the bias in a dataset by getting a representative number of records for each country or host (Figure 2). Continue reading “Download Randomized Data Subset from NCBI Virus”
NCBI Virus Extends Dashboard Visualizations to all Virus Sequences!
Do you want to be able to quickly filter your virus search results based on important attributes? Good news, now you can! We are pleased to announce the extension of Dashboard Visualizations for any virus in the NCBI Virus collection (Figure 1). Dashboard Visualizations allow data to be quickly visualized in a graphical presentation based on a few highly sought-after attributes to prefilter your dataset.
What are Dashboard Visualizations?
Dashboard Visualizations allow you to filter your search by geographic location, collection time, and release time. Each feature on the Dashboard is interactive, so when a filter is applied, it limits the data shown in the other features. When using these filters, the top summary section updates to provide you a snapshot of the number of records in NCBI RefSeq, Nucleotide, and Protein that fit the combined conditions of your search in the NCBI Virus database. Continue reading “NCBI Virus Extends Dashboard Visualizations to all Virus Sequences!”
Coming soon! Changes to NCBI Datasets command-line tool in version 14 (CLIv14.0.0)
In October 2022, NCBI Datasets will release version 14 of our datasets and dataformat command-line tools. This release will contain breaking changes to the command syntax, content of the data packages and data reports. Thank you for your feedback that inspired these new features. We hope they will improve your experience!
We will continue to support CLI v13.x, although new features and improvements will be exclusive to CLI v14.0.0 release and up.
NCBI Datasets supports the NIH Comparative Genomics Resource (CGR), an NLM project to establish an ecosystem to facilitate reliable comparative genomics analyses for all eukaryotic organisms. Join our mailing list to keep up to date with NCBI Datasets and other CGR news.
More details
How is version 14 of the Datasets command-line tools (CLI v14.x) different from CLI v13.x and previous versions? Continue reading “Coming soon! Changes to NCBI Datasets command-line tool in version 14 (CLIv14.0.0)”