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. 2013 Dec 30;42(6):e42. doi: 10.1093/nar/gkt1326

Figure 2.

Figure 2.

Using PROGNOS to identify nuclease off-target sites. (A) Outline of the procedure to identify nuclease off-target activity. (B) Sample outputs of the PROGNOS online software showing all sites found and what types of genomic regions they are located in as well as rankings of the top potential off-target sites. The rankings include the closest gene, the number of mismatches, the size of PCR product from the automatically designed primers, and other helpful information. (C) Comparison of the success of the automatically designed PROGNOS primers used in high-throughput full-plate PCR of off-target sites to primers designed in other off-target publications. (D) Sequencing reads of an off-target location for the 3F ZFN pair that show evidence of NHEJ. In the wild-type (WT) sequence, the ZFN binding sites are highlighted in yellow and mismatches to the intended target sequence are lowercase red. In the sequencing reads, inserted bases are lowercase and highlighted in blue. The size of the indel is displayed to the right of the sequence, along with the number of times that mutation was observed.