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. 2012 Jan;40(Database issue):D587-92.
doi: 10.1093/nar/gkr898. Epub 2011 Nov 7.

The LANL Hemorrhagic Fever Virus Database, a New Platform for Analyzing Biothreat Viruses

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Free PMC article

The LANL Hemorrhagic Fever Virus Database, a New Platform for Analyzing Biothreat Viruses

Carla Kuiken et al. Nucleic Acids Res. .
Free PMC article

Abstract

Hemorrhagic fever viruses (HFVs) are a diverse set of over 80 viral species, found in 10 different genera comprising five different families: arena-, bunya-, flavi-, filo- and togaviridae. All these viruses are highly variable and evolve rapidly, making them elusive targets for the immune system and for vaccine and drug design. About 55,000 HFV sequences exist in the public domain today. A central website that provides annotated sequences and analysis tools will be helpful to HFV researchers worldwide. The HFV sequence database collects and stores sequence data and provides a user-friendly search interface and a large number of sequence analysis tools, following the model of the highly regarded and widely used Los Alamos HIV database [Kuiken, C., B. Korber, and R.W. Shafer, HIV sequence databases. AIDS Rev, 2003. 5: p. 52-61]. The database uses an algorithm that aligns each sequence to a species-wide reference sequence. The NCBI RefSeq database [Sayers et al. (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 39, D38-D51.] is used for this; if a reference sequence is not available, a Blast search finds the best candidate. Using this method, sequences in each genus can be retrieved pre-aligned. The HFV website can be accessed via http://hfv.lanl.gov.

Figures

Figure 1.
Figure 1.
Tabular results page from the regular search interface, including functions available for the search results (phylogenetic tree, geographical information, etc.), ancillary information about sample background, genome coverage and taxonomic relations of the viral species.
Figure 2.
Figure 2.
Distribution of genomic sequence information over the flavivirus model genome, by viral species. For dengue, approximately 3500 complete genomes are available; the most densely sequenced region is nucleotides 800–2000, roughly corresponding to the envelope protein.
Figure 3.
Figure 3.
Geographical distribution of all sequences with geographical origin information in the Flavivirus genus in the HFV database.
Figure 4.
Figure 4.
Output from Highlighter tool, showing mutations Single Nuleotide Polymorphisms (SNPs) relative to a reference or ‘master’ sequence; in this case, a user input sequence of the species Chikungunya.

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