Virus hunting in the cloud: A hackathon story at ASV 2019


Are you going to ASV 2019?

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 hope to see you there!

Genome context graphic now in virus search results


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.Virus_searchFigure 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!

New Norovirus GenBank Submission Service


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
Submisssion_portal

Figure 1. The submission portal page showing the new option for submitting Norovirus data.

Begin a new Norovirus submission or see how to get started submitting other data to GenBank.

GenBank accepts a wide range of data to support scientific discovery and analysis on sequences from all branches of life.

Virus Hunting Data Science Hackathon next week in San Diego


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.

5 NCBI articles in 2018 Nucleic Acids Research database issue


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.

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NCBI’s Virus Variation Resource Enhancements Include Standardized Search Criteria


NCBI’s Virus Variation resource makes it easy to find genome and protein sequences for a number of viruses – no more stumbling through multiple synonyms to find what you need. Now you can search using standardized biological criteria and intuitive pull-down menus.

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NCBI researchers and collaborators discover novel group of giant viruses


Nearly complete set of translation-related genes lends support to hypothesis that giant viruses evolved from smaller viruses

An international team of researchers, including NCBI’s Eugene Koonin and Natalya Yutin, has discovered a novel group of giant viruses (dubbed “Klosneuviruses”) with a more complete set of translation machinery genes than any virus that has been described to date. “This discovery significantly expands our understanding of viral evolution,” said Koonin. “These are the most ‘cell-like’ viruses ever identified. However, the computational analysis of the virus genomes shows that these viruses have not evolved from cells by reductive evolution but rather have evolved from smaller viruses, gradually acquiring genes from their hosts at different stages of their evolution.”

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