Abstract: The present invention provides methods for site-specifically integrating at least one first nucleic acid into a genome of at least one cell, comprising: transforming said genome with a reporter nucleic acid construct that is linked to a first att site; selecting at least one first transformed cell having at least one integrated reporter nucleic acid construct; introducing said at least one first nucleic acid and a homologous recombination mediating enzyme into said cell wherein said at least one first nucleic acid comprises at least one second att site that is complementary to said first att site; and maintaining said cell under conditions sufficient for said at least one first nucleic acid to integrate into said first att site producing at least one stably integrated cell.