Host factors such as a previous infection with a heterologous DENV serotype, and virulence appear to play a role in determining disease severity in individuals [5–8]. Environmental factors like vector density, rainfall and temperature may affect the severity of DHF outbreaks [9]. Dengue viruses can be classified into 4 serotypes (DENV-1 to DENV-4) which have Selleck JQEZ5 a mean nucleotide identity of 70% between the serotypes and 95% within the serotypes. Figure 1 Dengue cases reported worldwide from 1955 to 2004. The number of dengue cases as reported in the WHO

DengueNet database [16] from 1955 to 2004. The number of DENV sequences available in the public sequence repositories has been growing steadily and the value of these sequences would be enhanced if exploratory analysis tools for performing preliminary phylogenetic analysis and search for epidemiological, geographic, and medical information were integrated with the database

and convenient interactive visualization was provided. DengueInfo [10] was developed by NITD as a resource for retrieving whole genomes and associated metadata. Similarly, whole genome sequences generated at the Broad Institute can be accessed and queried directly from the institute’s online database [11]. However, neither of these resources provide an integrated interface to analysis and visualization tools nor do they provide RG7420 molecular weight access to all dengue sequences irrespective of origin or length. To meet these needs, we extended the functionality developed by the authors of the NCBI Influenza Virus Resource to the non-segmented dengue virus. Since the DENV genome Janus kinase (JAK) is more than 4 times larger than the largest individual influenza virus segment, multiple sequence alignments could not be calculated on request as is done for influenza virus and are instead pre-calculated offline. The alignment calculation is a three step find more procedure

that first generates multiple protein alignments for the polyproteins derived from complete genome records of each DENV serotype, merges the serotype-specific protein alignments, and then iteratively adds shorter protein sequences. Coding sequence alignments are calculated on demand from the protein alignments. The new NCBI Virus Variation Resource is a flexible tool that can be extended to other viruses, for example West Nile virus. Construction and content Data sources and curation The current Virus Variation Resource includes dengue and influenza virus sequences. The NCBI Influenza Virus Resource was described elsewhere [1, 2]. Here we describe the extension of this resource to include dengue virus sequence data.