How Do I Access And Query Entire Genome Sequences (Salmonella Typhimurium LT2) With R

Question

[ctanui]

Is there a package in R where I can load in a whole genome of Salmonella Typhimurium LT2, and then say e.g. check the presence or absence of a given gene (ssrA)? or compare whole genomes of different strains against reference whole genome (Salmonella Typhimurium LT2) to check any similarity or differences, or another tool that you'd use for this job?