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PROGNOS Home Page
PROGNOS (Predicted Report Of Genome-wide Nuclease Off-target Sites) is an online tool to aid in the prediction and analysis of the off-target effects of engineered nucleases.
If you have used PROGNOS in the preparation of a paper, please cite it as described below:
Fine EJ, et al. An online bioinformatics tool predicts zinc finger and TALE nuclease off-target activity. Nucleic Acids Research, doi:10.1093/nar/gkt1326 (2013).



For help with using PROGNOS or interpreting the output, check out the Tutorials and FAQs sections of the website.

PROGNOS exhaustively searches a genome for sequences with a specified degree of homology to the intended target site, ranks the output, and designs PCR primers for high-throughput analysis.
----All PCR reactions can be done using the same thermocycler conditions in 96-well plates. The PCR success rate using PROGNOS designed primers is greater than 90%.
----Potential off-target sites are ranked and categorized by genomic region (exon, intron, promoter, intergenic) and a link is provided to view the site in the UCSC genome browser.

The following options help customize your search results:
  • Genome to search
  • Nuclease Type: Zinc Finger Nuclease (ZFN) or Transcription Activator-Like Effector Nuclease (TALEN)
  • Target sequence--degenerate IUPAC letters such as W, V, M, etc. are also allowed in addition to A G C T
  • Allowable spacer distances between binding sites
  • Maximum number of mismatches in each nuclease half-site
  • Allow homodimerization of nucleases
Parameters for the primer design can also be set to best fit your downstream analysis:
  • Primer melting temperature
  • Minimum distance from edge of amplicon to nuclease cleavage site
  • Minimum size difference between amplicon cleavage products


Example PROGNOS Search Results:
Before using PROGNOS to search a previously published pair of nucleases, check that it is not already available in this example list.
Gene TargetSpeciesNuclease Pair NameNuclease TypeReferencePROGNOS Results
CCR5Human CCR5-224 KK/ELZFNPattanayak et al. doi:10.1038/nmeth.1670 Click Here
VEGFHuman VF2468 KK/ELZFNPattanayak et al. doi:10.1038/nmeth.1670 Click Here
CCR5Human CCR5TALENMussolino et al. doi:10.1093/nar/gkr597 Click Here
IgMRat 101187/101188TALENTesson et al. doi:10.1038/nbt.1940 Click Here
AAVS1Human PPP1R12CTALENHockemeyer et al. doi:10.1038/nbt.1927 Click Here
kdrlZebrafish kdrl KK/ELZFNGupta et al. doi:10.1093/nar/gkq787 Click Here
tnikbZebrafish tnikbTALENHuang et al. doi:10.1038/nbt.1939 Click Here
N/AHuman I-SceIHoming Endonuclease Click Here
HBBHuman S2/S5 NNTALENFine et al. doi:10.1093/nar/gkt1326 Click Here
HBBHuman S2/S5 NKTALENFine et al. doi:10.1093/nar/gkt1326 Click Here
HBBHuman S1/S7 NNTALENFine et al. doi:10.1093/nar/gkt1326 Click Here
HBBHuman S1/S7 NKTALENFine et al. doi:10.1093/nar/gkt1326 Click Here
HBBHuman ZFN-3FZFNFine et al. doi:10.1093/nar/gkt1326 Click Here
HBBHuman ZFN-4FZFNFine et al. doi:10.1093/nar/gkt1326 Click Here



PROGNOS was created by Eli Fine
If you have comments or would like to see additional publicly available genomes added, please email EliFine@gatech.edu


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