foldgRNAs {CRISPRseek} | R Documentation |
Fold gRNAs with the gRNA backbone constant region and output minimum free energy and the folded structure in bracket notation using GeneRfold package
foldgRNAs(gRNAs.withoutPAM, gRNA.backbone="GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUUU", temperature = 37)
gRNAs.withoutPAM |
gRNAs as character, without PAM sequence. |
gRNA.backbone |
gRNA backbone constant region sequence. Default to the sequence in Sp gRNA backbone. |
temperature |
temperature in celsius. Default to 37 celsius. |
a data frame that contains a set of gRNAs annotated with bracket.notation (folded sgRNA in bracket notation), mfe.sgRNA (minimum free energy of sgRNA:gRNA plus backbone), mfe.diff (mfe.sgRNA-mfe.backbone), mfe.backbone (minimum free energy of the gRNA backbone by itself).
Lihua Julie Zhu
offTargetAnalysis
gRNAs.withoutPAM <- c("AACCTTGGGGTTACTGAAAG", "ATCCTGGAGCTTAGTCATAG") mfe <- foldgRNAs(gRNAs.withoutPAM)