The SNP map allows the user to navigate through SNP data sets obtained by NGS between a reference genome and several strains
The Snps are colored according to the mutation type and the gene/intergenic location. SNP types can be dynamically hidden and are mutually linked to cognate genes (e.g., when the mouse is over a gene, this triggers an animation of the enclosed and surrounding SNPs).
The snps are presented in a sub-map of the reference genome
Sequence variations (both at the nucleotide and protein levels) can be obtained .
The same color code is used to present the polymorphism. User can export the protein or dna sequence to a flat file.
, an artificial sequence can be determined across all genomes or for a group of genes
Either an artificial sequence is computed using all the SNP positions or the user can add genes to a gene basket that can subsequently be used to compute a subset artificial sequence. The sequence can be exported. The SNP is written in bold, the color is that of the gene the snp belongs to.
The user can build groups of strains (according to epidemiological, phylogenetic or other criteria) to obtain a SNP density map, i.e. a histogram where the size of the bars represents the number of SNPs per gene.
This view is connected to the local view: by clicking on a histogram's peak the user can go to the local view. The user is able to add a file to define the strain's group