CASSET_gRNA_designer
A library for gRNA design (for both single Cas and split-systems).
Split-system means 2 Cas (from the list: SpCas9, SaCas9, CjCas9, StCas9) are located in orientation (PAM-out, PAM-in, PAM-direct-forward, PAM-direct-reverse) with the condition: the angle between protein ends (N- or C-) less than 20 degrees.
Also, this library allows to design gRNA to recognize targets in a set of pathogens.
Pipeline:
Parameters that can be changed:
- permissible angle between 2 ends of Cas proteins for our set of the distance between 2 Cas
- manually set distance between 2 Cas
- number of mismatches in the first 12 nt and in the whole targets (for the task to detect several pathogens) for both left and right.
Examples
In example notebook you can find the following examples:
- search targets in N and E genes in Sars-Cov-2 genome for all variants of split-systems and for CasX
- search targets for NS5A gene and for all HCV genome for all variants of split-systems and for CasX
- search targets to detect 4 species of Borrelia simultaneously for all variants of split-systems
Under development
- On-target and off-targets scores for designed gRNAs, ranging of gRNAs
- BLAST check of organisms in which designed gRNAs could work
Attribution
- Code - A. Gribkova
- Distance between Cas proteins in split-systems from molecular modeling - R. Novikov, G. Armeev
- Logo - G. Armeev
