Virus Variation Resource—recent updates and future directions

@article{Brister2014VirusVR,
  title={Virus Variation Resource—recent updates and future directions},
  author={James Rodney Brister and Yīm{\'i}ng B{\`a}o and Sergey A. Zhdanov and Yuri Ostapchuck and Vyacheslav Chetvernin and Boris Kiryutin and Leonid Y. Zaslavsky and Michael Kimelman and Tatiana A. Tatusova},
  journal={Nucleic Acids Research},
  year={2014},
  volume={42},
  pages={D660 - D665}
}
Virus Variation (http://www.ncbi.nlm.nih.gov/genomes/VirusVariation/) is a comprehensive, web-based resource designed to support the retrieval and display of large virus sequence datasets. The resource includes a value added database, a specialized search interface and a suite of sequence data displays. Virus-specific sequence annotation and database loading pipelines produce consistent protein and gene annotation and capture sequence descriptors from sequence records then map these metadata to… 

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References

SHOWING 1-10 OF 17 REFERENCES

Virus variation resources at the National Center for Biotechnology Information: dengue virus

An offline pre-alignment procedure is developed which generates a multiple sequence alignment of all dengue sequences and is used to rapidly create alignments of sequence subsets in response to user queries.

Visualization of large influenza virus sequence datasets using adaptively aggregated trees with sampling-based subscale representation

This work developed an approach to visualize large phylogenetic trees in an aggregated form with a special representation of subscale details, which can be annotated using aggregation of structured metadata, such as seasonal distribution, geographic locations, etc.

The Influenza Virus Resource at the National Center for Biotechnology Information

The Influenza Genome Sequencing Project aims to rapidly sequence influenza viruses from samples collected all over the world, and in just over 2 years after the initiation of the project, more than 2,000 complete genomes of influenza viruses A and B had been deposited in GenBank.

The genomic and epidemiological dynamics of human influenza A virus

It is shown that the genomic evolution of influenza A virus is characterized by a complex interplay between frequent reassortment and periodic selective sweeps, suggesting a sink–source model of viral ecology in which new lineages are seeded from a persistent influenza reservoir to sink populations in temperate regions.

The International Nucleotide Sequence Database Collaboration

This article outlines INSDC services and update the reader on developments in 2011, including the newly launched BioProject database and improved handling of assembly information.

Phylogeography and population dynamics of dengue viruses in the Americas.

A "distance-informed" model, which posits that the intensity of virus movement between locations is inversely proportional to the distance between them, provided a better fit than a model assuming equal rates of movement between all pairs of countries, but for DENV-3 andDENV-4, the more stochastic "equal rates" model was preferred.

Continued Evolution of West Nile Virus, Houston, Texas, USA, 2002–2012

Inferred monophyletic relationships of these groups with several 2006–2009 northeastern US isolates supports potential introduction of a novel WNV strain in Texas since 2010 and emphasizes the need to maintain WNV surveillance activities to better understand WNV transmission dynamics in the United States.

West Nile virus: review of the literature.

In North America, West Nile virus has and will remain a formidable clinical and public health problem for years to come.

Challenges of global surveillance during an influenza pandemic

Nucleic Acids Research

The results suggest that overall polymerase activity fluctuates with a peak occurring at approximately early S phase, which indicates that DNA polymerase I is subject to a complex control and imply that it has a role in both DNA synthesis and DNA repair.