What is the Virus Variation resource?Virus variation is a specialized database and collection of tools which provide a number of unique features:
- Standardized annotation pipelines are used to produce consistent protein and gene annotation across all sequences from a given species.
- Automated and manual procedures capture sequence descriptors – metadata – from sequence records, literature, and other databases, map these to a common vocabulary, and store them with the sequences they describe.
- An enhanced search interface allows users to retrieve and download protein and nucleotide sequence sets based on a variety of biological criteria - like protein or gene of interest, genotype, host, collection country or region, disease severity, and collection date – as well as sequence patterns and key word searches.
- Specialized tools including a multi sequence alignment viewer and phylogenetic tree builder use precalculated alignments to rapidly analyze sequences selected by the user and retrieved from the database.
- An FTP site is available for bulk data retrieval.
- Virus specific BLAST databases are available.
Which virus species?Currently, there are dedicated resources for
Which sequences are available through the virus variation databases?
All Dengue and West Nile sequences deposited in DDBJ/EMBL/GenBank are reviewed for inclusion in the Virus Variation resource, but currently, two classes of sequences are excluded:
- Patent sequences
- Sequences found to be defective in some way. This may include sequences with frameshifts or vector sequence contamination.
To cite the Influenza Virus Resource, please refer to:
Bao Y., P. Bolotov, D. Dernovoy, B. Kiryutin, L. Zaslavsky, T. Tatusova, J. Ostell, and D. Lipman. The Influenza Virus Resource at the National Center for Biotechnology Information. J. Virol. 2008 Jan;82(2):596-601.
To cite the Dengue Virus Resource, please refer to:
Resch W., L. Zaslavsky, B. Kiryutin, M. Rozanov, Y. Bao, and T. A. Tatusova. The virus variation resources at the National Center for Biotechnology Information: dengue virus. BMC Microbiology 2009, 9:65.
Zaslavsky L, Y. Bao and T. A. Tatusova. Visualization of large influenza virus sequence datasets using adaptively aggregated trees with sampling-based subscale representation. BMC Bioinformatics, 2008;9:237.
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Zaslavsky L. and T. A. Tatusova. Accelerating the neighbor-joining algorithm using the adaptive bucket data structure. Bioinformatics Research and Applications. Lecture Notes in Computer Science, Springer-Verlag, 2008;4983:122-133.
Zaslavsky L, Y. Bao and T. A. Tatusova. Multiresolution approaches to representation and visualization of large influenza virus sequence datasets. IEEE International Conference on Bioinformatics and Biomedicine. 2007.
Bao Y, et al. FLAN: a web server for influenza virus genome annotation. Nucleic Acids Research. 2007 Jul 1;35(Web Server issue):W280-4.
Zaslavsky L, Y. Bao, and T. A. Tatusova. An Adaptive Resolution Tree Visualization of Large Influenza Virus Sequence Datasets. Bioinformatics Research and Applications. Lecture Notes in Computer Science, Springer-Verlag, 2007;4463:192-202.
Ghedin E, et al. Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature. 2005 Oct 20;437(7062):1162-6.
Holmes EC, et al. Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol. 2005 Sep;3(9):e300.
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