The invention relates to systems and methods for removing viral genetic sequences from host genomes by using a computer system to read a nucleotide string next to a protospacer adjacent motif (PAM) in the viral sequence, determine that the host genome lacks any region that matches the nucleotide string according to a predetermined similarity criteria and is adjacent to the PAM, and provide a guide sequence at least partially complementary to the nucleotide string. Providing the guide sequence may include synthesizing a guide RNA that includes a portion that is complementary to the nucleotide string.
