I have been working with reverse vaccinology of Rappuoli but only with a few genomes, thus the amount of data I have to analyze is small. Now I want to analyze a considerable number of genomes (more than 100). Do you have any suggestions on how to predict genomic islands (PAIs, RIs, SIs and MIs) for each genome and see the genes present in each island for this amount of data? This step of reverse vaccinology requires us to predict GIs because most vaccine targets are encoded within GIs. For a vaccine to be effective, the specific gene must be present in all strains/species that we are analyzing, thus it would be ideal if I could predict GIs and also see what is common between all the genomes. The current software that I use only analyzes one genome per run, it is really time consuming for big analyses.
Thank you for your attention.