We use the MUMmer program NUCmer to align genomic DNA or cDNA sequences from incomplete P. aeruginosa genomes or individual polymorphic sequences available at NCBI. SNPs and indels in non-repetitive regions are then identified by using the MUMmer program show-snps.
Once identified at the genomic level, polymorphisms are classified according to type of mutation (e.g. missense, silent, etc.) and its location within the gene's nucleotide and protein sequences, along with the downstream effect on the amino acid properties being recorded. Polymorphisms in genomic DNA, cDNA and amino acid sequences are also assigned a standardized description following recommendations made by the Human Genome Variation Society, a standard adopted by other SNP databases including dbSNP and Ensembl.
Access to this data is currently under the polymorphisms tab of any P. aeruginosa PAO1 gene (or gene card) page where an overview of point mutations is presented along with an image of the specific sequence containing hyperlinked mutations at each site (Figure 7 or oprD example). This page offers additional SNP information including the origin of the SNP call (e.g. experimental method such as restriction digest or computational prediction based on sequence alignment) to help provide users with a level of confidence regarding a given result. The nucleotides at these sites are coloured in order to distinguish synonymous (blue) and non-synonymous (red) mutations from insertions and deletions while a single strain can be selected from an adjacent list in order to apply a filter that hides all other strains.
Links are provided to more detailed point mutation descriptions, experimental details, sequence or alignment downloads and effects that a mutation would have on amino acid properties (Figure 8).
Links to a GBrowse genome viewer representation of the local genomic landscape is provided (Figure 9), whereby all known SNPs/indels are annotated and coloured by type. This presentation can be quite useful for visualizing regions undergoing a putatively higher degree of selection, as represented by a clustering of non-synonymous mutations.
Figure 9: GBrowse view of SNPs/Indels occurring in oprD gene of P. aeruginosa Br680.
White triangles: synonymous mutations. Red triangles: non-synonymous mutations. Black triangles: Insertions/deletions.
If you have any questions about the database or annotation, please feel free to contact us.