It may not be traditionally what you think of as flu season, but lately there’s been a great deal of talk about some viruses that are concerning public health officials and infectious disease specialists. You might have heard of the H7N9 situation in China, and the NCoV virus in France that made headlines.
But researchers are working all the time to understand, characterize, and evaluate viral sequences. They will access a number of different tools to do so. We talked last month about GISAID and EpiFlu as our Tip of the Week, and how the special access agreement they have developed has provided some otherwise reluctant governments to share the newest sequence data. So if you want the most current sequences–you would turn to EpiFlu.
There are other virus resources that you should investigate too. Another important site is the IRD, or Influenza Research Database. They have developed an extensive repository of many flu sequences, and have provided a wide range of tools to help researchers investigate and evaluate the data. In addition, they have incorporated some tools that provide novel analyses of the underlying data. This includes predictions of cytotoxic T-cell epitopes, and a sequence feature variant type analysis that they mention in their recent paper.
For this week’s video tip, I include their first of eight videos that will help you to understand their organization and tools. But be sure to keep going for the other 7 that they offer at their YouTube pages.
Be sure to also read the paper that they recently published–it has a nice overview of their tools, their strategies, and also provides a nice use case example of how to flow through a typical evaluation. And if you want other virus data besides flu check out the companion site Virus Pathogen Database and Analysis Resource. You’ll see a similar organization but with a wider range of sequences available. They have a separate thread of videos for the ViPR tools as well.
IRD, Influenza Research Database: http://www.fludb.org/
Other viruses not just flu are in the Virus Pathogen Resource (ViPR) that offers a similar structure and tools: http://viprbrc.org
Squires, R., Noronha, J., Hunt, V., García-Sastre, A., Macken, C., Baumgarth, N., Suarez, D., Pickett, B., Zhang, Y., Larsen, C., Ramsey, A., Zhou, L., Zaremba, S., Kumar, S., Deitrich, J., Klem, E., & Scheuermann, R. (2012). Influenza Research Database: an integrated bioinformatics resource for influenza research and surveillance Influenza and Other Respiratory Viruses, 6 (6), 404-416 DOI: 10.1111/j.1750-2659.2011.00331.x
Pickett, B., Sadat, E., Zhang, Y., Noronha, J., Squires, R., Hunt, V., Liu, M., Kumar, S., Zaremba, S., Gu, Z., Zhou, L., Larson, C., Dietrich, J., Klem, E., & Scheuermann, R. (2011). ViPR: an open bioinformatics database and analysis resource for virology research Nucleic Acids Research, 40 (D1) DOI: 10.1093/nar/gkr859