CHOPCHOP statistics

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Citations per year

Number of citations per year for the bioinformatics software tool CHOPCHOP

Tool usage distribution map

This map represents all the scientific publications referring to CHOPCHOP per scientific context
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Associated diseases

This word cloud represents CHOPCHOP usage per disease context

Popular tool citations

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CHOPCHOP specifications


Unique identifier OMICS_04700
Interface Web user interface
Restrictions to use None
Input data Gene, target region sequence
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes


  • person_outline Tessa G. Montague

Publications for CHOPCHOP

CHOPCHOP citations


Genome wide and high density CRISPR Cas9 screens identify point mutations in PARP1 causing PARP inhibitor resistance

Nat Commun
PMCID: 5945626
PMID: 29748565
DOI: 10.1038/s41467-018-03917-2

[…] In all, 29 sgRNAs were designed using the ChopChop algorithm. The guides were synthesised and cloned in an array format into pLentiGuide-puro by Eurofins genomics. A single colony for each vector was used to inoculate a pooled culture for pla […]


Chromatin accessibility is associated with CRISPR Cas9 efficiency in the zebrafish (Danio rerio)

PLoS One
PMCID: 5912780
PMID: 29684067
DOI: 10.1371/journal.pone.0196238

[…] Altogether, we have designed 86 sgRNAs using the, ChopChop (V1 and V2) and CRISPRscan softwares [,,]. Of these sgRNAs, 30% showed detectable in vivo activity (). As GC-content (%) has been suggested to influence the effectiveness of CRISPR-Cas9 mutag […]


Orientation dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome

Nat Commun
PMCID: 5899087
PMID: 29654302
DOI: 10.1038/s41467-018-03694-y

[…] ersions were induced using pairs of small guide RNAs (sgRNAs) that flank either most of the hinge region or only some of its elements (Supplementary Table ). The allele-specific sgRNAs designed using CHOPCHOP, were selected to include BL6 SNPs at the PAM site if available (Supplementary Fig. ; Supplementary Table ). Patski cells were transfected using Ultracruz transfection reagents (Santa Cruz). […]


Multiple sgRNAs with overlapping sequences enhance CRISPR/Cas9 mediated knock in efficiency

PMCID: 5938013
PMID: 29622782
DOI: 10.1038/s12276-018-0037-x

[…] Cas9 mRNAs were purchased from Toolgen (Seoul, Korea). sgRNAs for each gene were designed using CHOPCHOP and synthesized using an in vitro RNA-synthesis kit (Thermo Fisher Scientific, MA, USA) following PCR amplification. ssODNs were commercially designed and synthesized (IDT, CA, USA). The 3′ e […]


CRISPR/Cas9 Mediated Gene Disruption Reveals the Importance of Zinc Metabolism for Fitness of the Dimorphic Fungal Pathogen Blastomyces dermatitidis

PMCID: 5885028
PMID: 29615501
DOI: 10.1128/mBio.00412-18

[…] nd Biolabs, Ipswich, MA), and the sgRNA/protospacer regions of all targeting constructs were confirmed by Sanger DNA sequencing.Candidate protospacer sequences in the targeted genes were generated by CHOPCHOP (, ), and high-scoring candidates near the N-terminal region of the protein coding sequence were searched against the B. dermatitidis genome by using BLAST to eliminate candidates with obviou […]


Small molecules promote CRISPR Cpf1 mediated genome editing in human pluripotent stem cells

Nat Commun
PMCID: 5880812
PMID: 29610531
DOI: 10.1038/s41467-018-03760-5

[…] ALKBH1 has recently been identified as a tRNA demethylase. CLEC16A plays important roles in the development of diabetes. To construct gene-specific crRNA plasmids, we used an online software ( to design a panel of crRNAs specifically targeting these genes (Fig.  and Supplementary Table ). We tested the genome editing capacity of these crRNAs in 293T cells and observed 2 […]

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CHOPCHOP institution(s)
Computational Biology Unit, Department of Informatics, University of Bergen, Norway; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA; Sars International Centre for Marine Molecular Biology, University of Bergen, Norway
CHOPCHOP funding source(s)
Bergen Research Foundation; University of Bergen core funding; National Defense Science and Engineering Graduate Fellowship; American Cancer Society

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