Fourth Step. VIRGO verifies whether mismatches occur into double-stranded regions by creating a short reverse complementary sequences centered on the mismatch. VIRGO aligns the created sequence with a region of maximum 4001 nucleotides centered on the A-G mismatch. If the percentage of the alignment is greater than or equal to 85%, VIRGO annotates that mismatch as occurring into a double-strand region.
Distefano et al. BMC Bioinformatics 2013 14(Suppl 7):S5 doi:10.1186/1471-2105-14-S7-S5