Comparison of the genomic DNA of two strains is the standard technique for delineating prokaryotic species. Traditionally, the similarity value between two genomic DNAs was obtained by applying lab techniques that are laborious, hard to reproduce and can only be done in a few specialized laboratories. Moreover, the results obtained are not cumulative and do not allow the construction of a database.

In recent years, the development of mass sequencing and greater accessibility of genomic sequences makes it possible to calculate the similarity value between two genomes by comparing their genomic sequences. Thus, the values of the estimated DNA-DNA hybridization (eDDH) in silico or the Average Nucleotide Identity (ANI) can be calculated from the genomic sequences of a pair of strains.

Necessary material

Files with raw sequences obtained from full genome sequencing of the strains to be compared.

Methodology

The value of estimated DNA-DNA hybridization (eDDH) in silico is obtained from the free access GGDC program.

The Average Nucleotide Identity (ANI) value is obtained using the JSpecies program.