EuPaGDT

Eukaryotic Pathogen CRISPR guide RNA/DNA Design Tool

with (1) custom genome upload, (2) off-target analysis, (3) on-targets searching (for targeting gene families), (4) efficiency/activity prediction, (5) assisted oligo repair template design , (6) gRNA transcription problem identification, (7) flanking microhomology searching (for predicting deletions)

** Batch Mode **

upload and process multiple sequences in one run

if you are processing one gene, please use this link

A multi-thread version of batch mode is available upon request for analyzing >300 sequences

Job Name:

RNA/DNA guided
nuclease selection:(?)

choose one to automatically configure gRNA/gDNA and PAM settings for each nuclease

SpCas9
SaCas9
NgAgo
custom (please manually enter PAM requirement)

Additional option settings: (click to expand a category)

Batch process parameters

Number of top-ranking gRNAs
to collect for each sequence:


Only pick gRNA in conserved region:
Yes
No, use the whole input sequence

only identify gRNA in a region of input sequence: (?)
from beginning, % of length of input sequence

from end, % of length of input sequence

gRNA search parameters


gRNA length:  

PAM motif(s):
(use comma to separate multiple PAM motifs
use IUPAC code for degenerate base)

on-target search parameters

(Default settings
recommended for most users)


homology arm length:
identity:    
coverage:   

off-target search parameters

(Default settings
recommended for most users)


maximum number
of mismatches:

off-target PAM motif(s)(?):
(comma separated if more than one,
use IUPAC code for degenerate base)

HDR repair template parameters

(Default settings
recommended for most users)


homology arm length:(?)     

insertion:(?)    

Genome (expand a category and choose one):

genome naming paradigm:
specie strain database-version

Sequence:


or upload your fasta file here: 

(please use Chrome browser or enable Javascript in your browser for optimal results)