foldgRNAs {CRISPRseek}R Documentation

Fold gRNAs with the gRNA backbone constant region

Description

Fold gRNAs with the gRNA backbone constant region and output minimum free energy and the folded structure in bracket notation using GeneRfold package

Usage

foldgRNAs(gRNAs.withoutPAM, 
    gRNA.backbone="GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUUU",
    temperature = 37)

Arguments

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.

Value

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).

Author(s)

Lihua Julie Zhu

See Also

offTargetAnalysis

Examples

    gRNAs.withoutPAM <- c("AACCTTGGGGTTACTGAAAG", "ATCCTGGAGCTTAGTCATAG")
    mfe <- foldgRNAs(gRNAs.withoutPAM)

[Package CRISPRseek version 1.20.0 Index]