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DeepSpCas9-NG designs guide RNAs and predicts the efficiency of SpCas9-NG with conventional scaffold at endogenous cell target sites.
It supports the input of target sequences (at least 30bp) via FASTA format, and eight further formats: Gene Symbol, NMID, Ensembl ID, HGNC ID, a genomic position, an unedited/edited sequence pair, ClinVar ID and COSMIC ID.
Homology-directed repair (HDR) donor templates. When an input format describes an intended edit — an unedited/edited sequence pair, ClinVar ID or COSMIC ID — the results also carry what each guide needs for HDR: the cut site, the cut-to-edit distance, the donor template in the chosen type and orientation(s) (default: a single-stranded oligo on the sense strand, 100 nt homology arms each side), the realised arm lengths, an optional PAM-blocking mutation, and the candidate's rank among the target's guides. There is no HDR mode switch: the input format decides.
Note: DeepSpCas9variants provides guide RNA designs and efficiency predictions with optimized scaffold.
