GT-Scan is a generic pattern matching tool designed to identify occurances of a given motif within a given DNA sequence.

Subsequently, GT-Scan will search a reference genome for any matches or near-matches to these results.

Guided by a user-defined "rule" and "filter", GT-Scan can be catered to many popular genome editing technologies.


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 do these targets have in the genome?

Candidate targets are places in your genomic region that match the 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.