Finding optimal targets for genome editing or regulatory interference using CRISPR/Cas or zinc-finger nuclease systems.


Two questions GT-Scan can help answer are:

  1. What are the best candidate targets in my genomic region of interest?
  2. How many potential off-targets does the target I am using have in the genome?

Candidate targets are places in your genomic region that match a user-defined target rule. Potential off-targets are other places in the genome that are the same as the candidate target except for up to three mismatches, and that match a user-defined off-target filter.


GT-Scan finds each candidate target in your region of interest and reports:

  • the number of potential off-targets it has in the genome,
  • the genomic sequence and location of each potential off-target, and
  • how similar each potential off-target is to it.

GT-Scan sorts candidate targets by how many potential off-targets they have, rather than using a (possibly obscure) ranking formula. It sorts successively by the number of potential off-targets at four levels of increasing severity: 0, 1, 2 or 3 mismatches.

For each candidate target, GT-scan describes each of its potential off-targets reporting:

  • the total number of mismatches,
  • the number of low-specificity mismatches,
  • the number of high-specificity mismatches,
  • the positions of the mismatches, and
  • a link to the potential off-target in the Ensembl genome browser.

This information can help you decide on the best candidate target (Question 1) or evaluate a given target (Question 2).


GT-Scan lets you define a target rule that specifies

  • the length of candidate targets,
  • required letters in candidate targets (e.g., the 3'-NGG for CRISPR/Cas systems), and
  • the level of binding specificity (zero, low or high) at each position.

GT-Scan also lets you define an off-target filter. Potential off-targets that don't match the filter are ignored. For example, you can require off-targets to match either 3'-NAG or 3'-NGG for CRISPR/Cas systems.

GT-Scan can also ignore potential off-targets with more than a maximum number of high-specificity mismatches that you specify.

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March 2016 Added zebrafish genome GRCz10. Moved older genome versions to "Archived" section. January 2016 Added human genome GRCh38. November 2015 The service has been restored following an issue with submitting jobs. Sorry for the downtime and thank you for your patience! October 2015 Added support for rice, barley and maize genomes. June 2015 Added support for the S. aureus Cas9 PAM (NNGRRT). February 2015 Added support for the tomato genome (ITAG2.4). May 2014 GT-Scan is released! Feel free to contact us if you notice any problems or have questions.