If a gap column is inserted into the profile during one of the iterative alignment steps, it is introduced into the complete seed alignment of all types to preserve consistency. When new sequences are added to the VVR database, they are added to the existing alignment through the last step of the alignment procedure. Periodically, the alignment

is completely recalculated to take advantage of the increases ERK inhibitor in the number of complete sequences. Alignments are calculated with MUSCLE [12] driven by a set of custom Perl programs which rely on the BioPerl toolkit [13]. Nucleotide alignments of the coding regions are generated dynamically as codon alignments based on the protein alignments. Web interface and analysis tool construction The web interface is implemented using the NCBI C++ toolkit [14] and JavaScript. The JavaScript modules were adaptated from the NCBI Influenza Virus Resource and were described previously [1, 2]. C++ tools of the Influenza Virus Resource were extended to allow the use of pre-calculated dengue alignments. XAV-939 cell line Utility and discussion Database query interface Figure 3A shows the basic query interface

to the dengue virus database. Users may either search for protein sequences, their coding regions (CDS), or genomic nucleotide sequences. Additional searchable fields are: serotype (1 – 4), disease severity (DF, DHF, DSS), Country or region of isolation (e.g. Europe, Puerto Rico), isolation year or year range, the genome regions included in the sequence (e.g. C, M, E), or a substring of the sequence (e.g. MNNQRKKAKN). Results may be restricted to complete sequences. Each time a query is executed by clicking “”Add to Query Builder”", a summary of the query parameters and the number of results are shown in the Query Builder table. An arbitrary number of queries can be executed and results for any subset of the queries can be obtained by selecting them and clicking “”Get sequences”",

which will display the result view as seen in Figure 3B. Results can be ordered by up to three fields and a subset may be selected. The nucleotide, protein, or CDS sequence of the selected results can be downloaded in FASTA format. Alternatively, accession filipin lists can be obtained as well. Figure 3 Interface. (A) Dengue virus query form; (B) Results page for query; (C) Multiple alignment view for results; (D) Neighbor joining tree based on nucleotide distances of codon-aligned open reading frames. Dengue serotype 1 sequences are tagged with green markers. Large branches are aggregated. Multiple alignment viewer The multiple alignment viewer is accessible from the results view. It assembles the Selleck Linsitinib requested pre-aligned sequences and displays them with a measure of sequence variability and a consensus anchor sequence at the top (Figure 3C). Any of the sequences can be chosen to replace the consensus as the anchor.