If you use our resources please cite accordingly.
The criteria used for evaluation of sgRNA efficiency in PLATINUM CRISPR are based on the following manuscript:
Haussmann, I.U., Dix, T.C., Dezi, V., Hans, A., Arnold*, R. and Soller*, M. (2022) sgRNA structural constraints and genetic limitations for efficient Cas9 genome editing to generate knock-outs and gene replacements in a Drosophila model, bioRxiv
Use of sgRNA/Cas9 for plasmid DNA scission in vitro is described here:
Haussmann, I. U., Ustaoglu, P., Brauer, U., Hemani, Y., Dix, T. and Soller, M. (2019) Plasmid-based gap-repair recombineered transgenes reveal a central role for introns in mutually exclusive alternative splicing of Down Syndrome Cell Adhesion Molecule exon 4. Nucleic Acid Research 47:1389-1403.
The prediction software and web-server use the following software packages:
RNAFold from the ViennaRNA Package, web-server:RNA Fold
Lorenz, Ronny and Bernhart, Stephan H. and Honer zu Siederdissen, Christian and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F. and Hofacker, Ivo L. ViennaRNA Package 2.0 Algorithms for Molecular Biology, 6:1 26, 2011, doi:10.1186/1748-7188-6-26
bpRNA script to interprete secondary structure files:BPRNA Database
Danaee, Padideh, et al. "bpRNA: large-scale automated annotation and analysis of RNA secondary structure." Nucleic acids research 46.11 (2018): 5381-5394. https://doi.org/10.1093/nar/gky285