Table 1
Open in new tab

Web-based tools and command lines for pegRNA design

SoftwareSupported enzymeOff target analysisInputPrime design for pegRNA cloningSupport pegRNA design for plantSpecial featuresReferences
MulticrisprSpCas9Yes–NoYes–Bhagwat et al. (2020)
Prime editing design toolSpCas9 SpCas9-NGYes–NoNoDesigning pegRNAs for correcting pathogenic variants in ClinVar databaseMorris et al. (2020)
PnB DesignerSpCas9NoDNA sequence or genomic
coordinates		NoNo–Siegner et al. (2021)
PINE-CONESpCas9NoDNA sequence, edit types, PBS and RT lengthNoNo–Standage-Beier et al. (2021)
pegFinderSpCas9
SpCas9-NG
SpRY		Yes (not for plants)DNA sequenceYesYes_Chow et al. (2020)
PE-DesignerSpCas9
SpCas9-VQR
SpCas9-VRERSpCas9-NG		YesDNA sequenceNoYes–Hwang et al. (2021)
pegITSpCas9
SpCas9-NG
CjCas9
SaCas9
SaCas9-KKH		YesDNA sequence or genomic
coordinates		YesYes–Anderson et al. (2021)
Easy-PrimeSpCas9NoDNA sequenceNoYesConsidering pegRNA secondary structure and predicting the prime editing efficiencyLi et al. (2021e)
PrimeDesignSpCas9Yes (not for plants)DNA sequenceNoYesCalculating pegRNA secondary structure and designing pegRNAs for saturation mutagenesisHsu et al. (2021)
DeepPESpCas9NoDNA sequenceNoYesPredicting the prime editing efficiencyKim et al. (2021)
PlantPeg DesignerSpCas9
SpCas9-NG Cas9 orthlogs		NoDNA sequenceYesYesDesigning dual pegRNAsLin et al. (2021)
SoftwareSupported enzymeOff target analysisInputPrime design for pegRNA cloningSupport pegRNA design for plantSpecial featuresReferences
MulticrisprSpCas9Yes–NoYes–Bhagwat et al. (2020)
Prime editing design toolSpCas9 SpCas9-NGYes–NoNoDesigning pegRNAs for correcting pathogenic variants in ClinVar databaseMorris et al. (2020)
PnB DesignerSpCas9NoDNA sequence or genomic
coordinates		NoNo–Siegner et al. (2021)
PINE-CONESpCas9NoDNA sequence, edit types, PBS and RT lengthNoNo–Standage-Beier et al. (2021)
pegFinderSpCas9
SpCas9-NG
SpRY		Yes (not for plants)DNA sequenceYesYes_Chow et al. (2020)
PE-DesignerSpCas9
SpCas9-VQR
SpCas9-VRERSpCas9-NG		YesDNA sequenceNoYes–Hwang et al. (2021)
pegITSpCas9
SpCas9-NG
CjCas9
SaCas9
SaCas9-KKH		YesDNA sequence or genomic
coordinates		YesYes–Anderson et al. (2021)
Easy-PrimeSpCas9NoDNA sequenceNoYesConsidering pegRNA secondary structure and predicting the prime editing efficiencyLi et al. (2021e)
PrimeDesignSpCas9Yes (not for plants)DNA sequenceNoYesCalculating pegRNA secondary structure and designing pegRNAs for saturation mutagenesisHsu et al. (2021)
DeepPESpCas9NoDNA sequenceNoYesPredicting the prime editing efficiencyKim et al. (2021)
PlantPeg DesignerSpCas9
SpCas9-NG Cas9 orthlogs		NoDNA sequenceYesYesDesigning dual pegRNAsLin et al. (2021)

Note: The dash in the table indicates that the data are not available.

Table 1
Open in new tab

Web-based tools and command lines for pegRNA design

SoftwareSupported enzymeOff target analysisInputPrime design for pegRNA cloningSupport pegRNA design for plantSpecial featuresReferences
MulticrisprSpCas9Yes–NoYes–Bhagwat et al. (2020)
Prime editing design toolSpCas9 SpCas9-NGYes–NoNoDesigning pegRNAs for correcting pathogenic variants in ClinVar databaseMorris et al. (2020)
PnB DesignerSpCas9NoDNA sequence or genomic
coordinates		NoNo–Siegner et al. (2021)
PINE-CONESpCas9NoDNA sequence, edit types, PBS and RT lengthNoNo–Standage-Beier et al. (2021)
pegFinderSpCas9
SpCas9-NG
SpRY		Yes (not for plants)DNA sequenceYesYes_Chow et al. (2020)
PE-DesignerSpCas9
SpCas9-VQR
SpCas9-VRERSpCas9-NG		YesDNA sequenceNoYes–Hwang et al. (2021)
pegITSpCas9
SpCas9-NG
CjCas9
SaCas9
SaCas9-KKH		YesDNA sequence or genomic
coordinates		YesYes–Anderson et al. (2021)
Easy-PrimeSpCas9NoDNA sequenceNoYesConsidering pegRNA secondary structure and predicting the prime editing efficiencyLi et al. (2021e)
PrimeDesignSpCas9Yes (not for plants)DNA sequenceNoYesCalculating pegRNA secondary structure and designing pegRNAs for saturation mutagenesisHsu et al. (2021)
DeepPESpCas9NoDNA sequenceNoYesPredicting the prime editing efficiencyKim et al. (2021)
PlantPeg DesignerSpCas9
SpCas9-NG Cas9 orthlogs		NoDNA sequenceYesYesDesigning dual pegRNAsLin et al. (2021)
SoftwareSupported enzymeOff target analysisInputPrime design for pegRNA cloningSupport pegRNA design for plantSpecial featuresReferences
MulticrisprSpCas9Yes–NoYes–Bhagwat et al. (2020)
Prime editing design toolSpCas9 SpCas9-NGYes–NoNoDesigning pegRNAs for correcting pathogenic variants in ClinVar databaseMorris et al. (2020)
PnB DesignerSpCas9NoDNA sequence or genomic
coordinates		NoNo–Siegner et al. (2021)
PINE-CONESpCas9NoDNA sequence, edit types, PBS and RT lengthNoNo–Standage-Beier et al. (2021)
pegFinderSpCas9
SpCas9-NG
SpRY		Yes (not for plants)DNA sequenceYesYes_Chow et al. (2020)
PE-DesignerSpCas9
SpCas9-VQR
SpCas9-VRERSpCas9-NG		YesDNA sequenceNoYes–Hwang et al. (2021)
pegITSpCas9
SpCas9-NG
CjCas9
SaCas9
SaCas9-KKH		YesDNA sequence or genomic
coordinates		YesYes–Anderson et al. (2021)
Easy-PrimeSpCas9NoDNA sequenceNoYesConsidering pegRNA secondary structure and predicting the prime editing efficiencyLi et al. (2021e)
PrimeDesignSpCas9Yes (not for plants)DNA sequenceNoYesCalculating pegRNA secondary structure and designing pegRNAs for saturation mutagenesisHsu et al. (2021)
DeepPESpCas9NoDNA sequenceNoYesPredicting the prime editing efficiencyKim et al. (2021)
PlantPeg DesignerSpCas9
SpCas9-NG Cas9 orthlogs		NoDNA sequenceYesYesDesigning dual pegRNAsLin et al. (2021)

Note: The dash in the table indicates that the data are not available.

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