Add option/PAM for Staphylococcus aureus Cas9?

[photocyte]

Hi there,

I'm wondering if it might be possible to add Staphylococcus aureus Cas9 (SaCas9) to FlashFry? It has a canonical NNGRRT PAM motif, with the NNGRRN motif showing quite significant nuclease targetting as well.

SaCas9 is a small Cas9 ortholog, so it is starting to be published on more and more for space limited applications (i.e. AAV viral vectors and gene therapy applications). Here is an example:

Y. Tan et al., “Rationally engineered Staphylococcus aureus Cas9 nucleases with high genome-wide specificity,” Proceedings of the National Academy of Sciences, vol. 116, no. 42, pp. 20969–20976, Oct. 2019, doi: 10.1073/pnas.1906843116.

and discovery paper:
F. A. Ran et al., “In vivo genome editing using Staphylococcus aureus Cas9,” Nature, vol. 520, no. 7546, Art. no. 7546, Apr. 2015, doi: 10.1038/nature14299.

I did try to look into the code to submit a PR. I assume this is the place, but I don't know Scala, and the use of bitwise operations comments like this gave me some pause :x

FlashFry/src/main/scala/standards/StandardScanParameters.scala

Line 98 in 127a455

// be super careful with this value!! the cas9 mask only considers the lower 46 bites (23 of 24 bases are used)