While alignments in the Influenza Resource are calculated on demand, dengue alignments are pre-calculated to increase responsiveness and reduce server loads. Details of this approach are described in a later HM781-36B purchase section. All DENV nucleotide and protein sequences available in the public DDBJ/EMBL/GenBank repositories are evaluated for inclusion in the database.

Patent sequences and sequences that contain obvious errors or vector sequences are excluded and the serotype classification is verified by comparison with a reference sequence set. Metadata (disease severity, collection date, collection location, serotype, genome region) are taken from the records, if available, or obtained from the literature. The region of the

DENV genome covered by the sequence is determined by alignment and made available for queries. Newly public sequences are detected in the NCBI data stream daily and are usually added to the database within a week of becoming available. Data overview Currently there are 6235 DENV records available in the VVR and the available metadata are summarized in Table 1. The number selleck chemical of sequence records available increases roughly exponentially with the year of collection (Figure 2A). The most sequenced region of the dengue genome is E and the majority of sequences are short (< 500 nt), however, there is a growing number of complete genomes available (Figure 2B, C), in large part due to the active effort to collect world-wide genome sequences. As expected, three of the top 5 most frequently represented countries in the VVR database are Asian (Taiwan, Thailand, and Viet Nam). The others are North and South American, respectively (Puerto Rico and Brazil; see Figure 2D). Figure 2 Data overview. Frequency of (A) collection years (N = 4543), (B) genome regions (N = 6235), (C) sequence lengths (N = 6235), and (D) collection countries (N = 5635) for dengue records in VVR. Table 1 Data overview Data overview Total dengue records 6235    known collection Country 5635 (90%)    known Ribociclib collection year 4543 (73%)    known disease severity 1604 (26%) Serotypes      DENV-1 1717 (28%)    DENV-2 2000 (32%)    DENV-3 1870 (30%)

   DENV-4 648 (20%) Overview of the characteristics of dengue records available in VVR Database construction Virus Variation Resource data are stored in the relational database system MSSQL Server 2005 using a simple schema that stores nucleic acid sequences and their metadata in one table and protein sequences in a second table linked to their encoding sequences through an id field. Alignment construction Multiple alignments of the available DENV protein sequences in VVR are pre-calculated offline using the following three step procedure. First, all complete protein sequences of each serotype are aligned separately in a multiple alignment step. Then, the individual intra-type alignments are merged to create a seed alignment covering the complete dengue polyprotein.