The RNA Virus Database

Belshaw, Robert; de Oliveira, Tulio; Markowitz, Sidney; Rambaut, Andrew

Our site allows virus nucleotide or amino acid sequences submitted by the user to be identified or, if the query is a new species, its closest relative to be found. In addition, the genomic location of any matched region of the library sequences is shown. For this we use NCBI's suite of BLAST programs (16) (go to the 'BLAST' link on the toolbar of the home page). Once the most closely related reference species has been located, the query sequence can then be placed into a whole-genome multiple alignment for that species (where such an alignment is present) in order to show the query's phylogenetic relationships to the genomes in our database (go to 'Align your sequence' on the virus species main page). An example of this process is illustrated in Figure 2 . Two procedures are available here for building the new multiple alignment. (i) A BLAST of the query to the reference species sequence provides coordinates from the resulting pair-wise alignment. These coordinates are then used to select homologous regions from the reference multiple alignment, and a new multiple alignment is then built using ClustalW along with a phylogenetic tree using PAUP as described above. (ii) BlastAlign (described above) is used to generate a new multiple alignment using the query sequence plus the sequences from the reference multiple alignment.