Table 1 |.
Comparison of in silico off-target site search tools for ZFNs and TALENs
| Name | Screening approach or algorithm | Off-target ranking/scoring basis | Strengths | Weaknesses |
|---|---|---|---|---|
| ZFN tools | ||||
| PROGNOS78 (website) | Base by base | Weighted homology, conserved G score and polarity effects | Allows user-defined spacing, ZF homodimerization and ambiguous bases. Analyzes ZF subunits. Relatively low false-positive ratios | Limited training set |
| ZFN-site128 (website) | TagScan129 | Sequence homology | Allows user-defined spacing, ZF homodimerization and ambiguous bases | No scoring algorithm |
| Zinc finger tools130 (website) | Search in <10-kb user-defined sequence | N/A | Screens ZF targets in user-supplied DNA sequences | Screens limited to 49 triplets with validated ZF domains |
| TALEN tools | ||||
| PROGNOS78 (website) | Base by base | Modular position weight matrix, binding energy compensation, polarity effects | Allows up to 20 mismatches. Relatively low false-positive ratios (∼11:1)a | Limited training set |
| CHOPCHOP62 (website) | Bowtie | Weighed off-target site number | Allows up to two mismatches | Potentially misses off-target sites |
| TALENgetter/, TALENoffer76 (website, command line) | Base by base with threshold-based speed-up strategy | Machine-learning-based modular position weight matrix | Allows up to ten mismatches; allows the use of rare RVDs | Scoring algorithm not as accurate as PROGNOS78 |
| TALE-NT 2.0 (ref. 75; website) | Base by base | Modular position weight matrix | The first scoring tool for TALEN off-target analysis | Potential worse performance if using custom RVD designs |
a
The false-positive ratios are defined as ‘the number of screened sites with no detectable activity to the number with detectable activity measured by experimental prediction methods’78.