It 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.
— Vincent Racaniello (@profvrr) February 11, 2016
Viral Resources at NCBI: http://www.ncbi.nlm.nih.gov/genome/viruses/
Virus Variation Resource: http://www.ncbi.nlm.nih.gov/genome/viruses/variation/
Brister, J., Ako-adjei, D., Bao, Y., & Blinkova, O. (2014). NCBI Viral Genomes Resource Nucleic Acids Research, 43 (D1) DOI: 10.1093/nar/gku1207