Tag Archives: viral genomes

Viral Genomes at NCBI

Video Tip of the Week: Viral Resources at NCBI (including new #ZikaResearch module)

Viral Genomes at NCBIIt would be hard to escape hearing and reading about the recent drama about the Zika virus. But in terms of viral genomics, that only serves to highlight how important it is to deliver quality sequence information for researchers. So in a timely coincidence, a recent lecture for the CDC on the Viral Resources at NCBI was just made available.

The lecture by Rodney Brister provides an overview of the features of the site and explores ways to access the data with some tools they’ve had in place for a long time. He shows ways to quickly get to family members. Then he described a newer direction that they are taking that includes a separate feature accessed from the same homepage called the Virus Variation Resource (starts ~11min). If you click through you’ll see that there are modules for various viruses–and a Zika module just became available last week. So you can find sequences collected there, and also links to related health resources like the WHO and CDC relevant pages. (That’s not shown in the webinar, which was recorded in December 2015). He shows a dengue example that’s got some additional features too.

There’s also a Retrovirus Resource available (~25min in), which offers “specialized tools for the analysis of retroviral proteins and genomes”. And that’s the place to go if you want the HIV-1 specific module, it’s not with the others that I mentioned before.

It’s longer than our typical tips–but it’s worth exploring if you want to refine your skills at quickly getting to virus data and tools. Just a quick word about a question they had towards the end–about bacteriophage resources. There’s a resource I particularly like for phages, which you can find here: http://www.phisite.org .

Special note: if you intend to use the AmazonAWS services for any viral genome analysis, you should be aware of this.

Quick links:

Viral Resources at NCBI:  http://www.ncbi.nlm.nih.gov/genome/viruses/

Virus Variation Resource: http://www.ncbi.nlm.nih.gov/genome/viruses/variation/

Zika module: http://www.ncbi.nlm.nih.gov/genome/viruses/variation/Zika/


Brister, J., Ako-adjei, D., Bao, Y., & Blinkova, O. (2014). NCBI Viral Genomes Resource Nucleic Acids Research, 43 (D1) DOI: 10.1093/nar/gku1207

Quick intro to Viral Bioinformatics Resource Center

I just spent a bit over an hour getting some one-on-one time with Chris Upton at Viral Bioinformatics Resource Center. He was showing me the tools and resources they have (we used the new screensharing iChat feature of Leopard OS 10.5, that alone was worth the cost of upgrading to 10.5 this week, or even dumping your PC and getting a Mac ;-)… but I digress…) and they look quite useful. You can analyze a large number of viral genomes in their database (or upload your own, or a bacterial genome for that matter) in many different ways. Their webpage navigation and look is going to change soon (and I’ll inform you when it does), but the software and tools will remain the same (they are mainly Java programs), so if you want, you can go check them out. I suggest starting with VOCS which is a sort of an advanced search/filter/browser for viral genomes and from which you can access several other of the tools. We’ll be looking at these tools more in depth (I have a couple tips planned for the near future, tutorial), but thought I’d point it out to you now. Quite nice.