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Br
eaking
20
Ca
s
Breaking-Cas
Oligo guide design tool for CRISPR based genome editing.
Breaking Cas sever is maintained since 2020 by Juan Antonio García-Martín
Please cite:
"Juan C. Oliveros, Mònica Franch, Daniel Tabas-Madrid, David San-León, Lluis Montoliu, Pilar Cubas and Florencio Pazos (2016). Breaking-Cas––interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes.
Nucleic Acids Research (2016) doi: 10.1093/nar/gkw407
. https://bioinfogp.cnb.csic.es/tools/breakingcas
"
Tutorial
1
Choose organism: (
alphabetic list
)
pepe
Write 3 letters or more and select it.
2
Paste one or several query DNA sequences in FASTA format (up to 20,000 nucleotides in total):
Or upload FASTA file (DNA):
3
Select nuclease settings:
Select Cas nuclease
Custom
Cas9:
Streptococcus pyogenes
Cas9 (SpCas9) (PAM: "NGG" in 3')
Cas9:
Streptococcus pyogenes
Cas9 (SpCas9) (PAM: "NAG or NGG" in 3')
Cas9:
Staphylococcus aureus
Cas9 (SaCas9) (PAM: "NNGRRN" in 3')
Cpf1/Cas12a:
Acidaminococcus sp. BV3L6
(AsCpf1-WT) (PAM: "TTTV" in 5')
Cpf1/Cas12a: (RVR variant)
Acidaminococcus sp. BV3L6
(AsCpf1-RVR) (PAM: "TVTV" in 5')
Cpf1/Cas12a: (RR variant)
Acidaminococcus sp. BV3L6
(AsCpf1-RR) (PAM: "TYCV" in 5')
xCas9:
Evolved spCas9 variants (Nature, 2018)
MAD7: Cas12a variant from
Eubacterium rectale
(PAM: "YTTN" in 5')
Or set your own parameters:
PAM sequence:
Use predefined settings for Cas9 or Cpf1, or set custom parameters for other nucleases. If necessary, write a different PAM sequence (in IUPAC notation). For Cas9, positional weights based on Hsu et al. (2013) are used by default. See
tutorial pages
for details on off-targets score's calculation.
PAM position:
5'
3'
Guide length:
18 nts.
19 nts.
20 nts.
21 nts.
22 nts.
23 nts.
24 nts.
25 nts.
Mismatches:
Up to 4
Up to 3
Up to 2
Up to 1
pepe
Confirmation email (optional):
To receive a message as soon the job finishes.
Write it carefully
(it will not be checked).
Fill with example
Clear fields
BioinfoGP, Centro Nacional de Biotecnología (CNB-CSIC)