Let us assume that genomic sequences G1 and G2 are associated to antibiotic resistant bacterial strains, while genomic sequences G3 and G4 are derived from bacterial strains sensitives to this antibiotic (genomic sequences G1, G2, G3 and G4 are stored in tests directory).
The objective here is to search for specific sequences than can be involved in antibiotic resistance in genomes G1 and G2.
To do so, we first create a list file with the paths of genomic sequences that belong to antibiotic resistance strains (inGroupTest.txt). And a list file with the paths of genomic sequences that not belong to antibiotic resistance strains (outGroupTest.txt).
SkIf2 search for specific k-mers (in this example length = 24) of genomes G1 and G2 :
cd tests ../build/bin/SkIf2 -inGroupFile inGroupTest.txt -outGroupFile outGroupTest.txt -k 24 -outputPrefix specificInGroup
Check outputs :
We can also observe that these 2 specific long-mers overlapped.
As G1 and G2 are antibiotic resistant bacterial strain, we can postulate that the CDS involved in this trait is probably located in this long fragment.