As of this release (1.0), ICE assumes you are using S.pyogenes Cas9. However, it does not check if the PAM site is NGG and just uses the input guide sequence to place the predicted cutsite 3bp upstream of the end of the input sequence. If you wish to analyze other nucleases, you can input a fake guide sequence and position your expected cut site 3bp from the end of your sequence. This guide sequence will be used by the tool and the algorithm does not enforce any particular PAM site. We will add explicit support of other nucleases in upcoming versions of ICE.
Articles in this section
- How do I use the ICE analysis tool and interpret my results?
- How many samples can ICE analyze at once?
- What RNA-guided nucleases does ICE analysis support?
- What size PCR amplicons should I use for ICE and ICE-D analysis tool? How should I design my PCR primers?
- Are there parameters that I can specify, such as indel window or expected cutting site?
- Can I run ICE on a private server or in the cloud?