ProtospacerWB statistics

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Citations per year

Number of citations per year for the bioinformatics software tool ProtospacerWB

Tool usage distribution map

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


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ProtospacerWB specifications


Unique identifier OMICS_09588
Name ProtospacerWB
Alternative name Protospacer Workbench
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data Genomic regions of interest (targets) of any organism
Output data Optimised guide-RNA designs for one or more target regions of interest
Operating system Mac OS
Programming languages Python
Parallelization OpenCL
Computer skills Medium
Version 1.0
Stability Stable
Maintained Yes


  • Bacteria
    • Escherichia coli
    • Mycoplasma pneumoniae
  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Plants and Fungi
    • Arabidopsis thaliana
    • Saccharomyces cerevisiae
    • Zea mays
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio
    • Xenopus laevis


No version available



Publication for Protospacer Workbench

ProtospacerWB citations


The Plasmodium falciparum rhoptry protein RhopH3 plays essential roles in host cell invasion and nutrient uptake

PMCID: 5365315
PMID: 28252384
DOI: 10.7554/eLife.23239.017

[…] ing a recodonized form of rhopH3 exons 4–6. The complete native sequences of exons 3 and 7 were included on either side of this central module to act as flanking regions for homology-directed repair. Protospacer Workbench () was used to identify 20 bp protospacer sequences specifically targeting rhopH3. To generate pSgRNA plasmids expressing suitable sgRNAs, InFusion-based cloning (Clontech, Mount […]


Rapid Generation of Marker Free P. falciparum Fluorescent Reporter Lines Using Modified CRISPR/Cas9 Constructs and Selection Protocol

PLoS One
PMCID: 5172577
PMID: 27997583
DOI: 10.1371/journal.pone.0168362

[…] /HindIII, resulting in intermediate plasmids CM162 and CM163. A guide sgRNA (sgRNA2) sequence for Pf230p was identified using the Protospacer software (alpha version; and was amplified using the primers P7/P8. This sgRNA was selected based on the best off targets hits score throughout the genome given by Protospacer and the total numbe […]


Plasmodium falciparum PfSET7: enzymatic characterization and cellular localization of a novel protein methyltransferase in sporozoite, liver and erythrocytic stage parasites

Sci Rep
PMCID: 4763181
PMID: 26902486
DOI: 10.1038/srep21802

[…] The CRISPR/Cas9 genome editing approach was employed to generate HA-tagged PfSET7 transgenic parasite line as described previously. We used Protospacer Workbench to identify sgRNA sequences for PfSET7 and computationally predict off-target sites. A 20-nt gRNA target sequence (5′-CACTGATGCTCCTCAAATTG-3′) directing Cas9 cleavage near the C- […]


Minimizing off Target Mutagenesis Risks Caused by Programmable Nucleases

Int J Mol Sci
PMCID: 4632775
PMID: 26501275
DOI: 10.3390/ijms161024751

[…] icity.Most of the online tools have a low throughput to design multiple sgRNAs, and available organisms are limited. However, recently developed off-line software, such as CasOT [], sgRNAcas9 [], and Protospacer Workbench [], have greater flexibility to select targets from any organism where a genomic sequence is available. Offline software provide greater flexibility and computational speed, but […]

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ProtospacerWB institution(s)
Biology of Host-Parasite Interactions Unit, Institut Pasteur, Paris, France; CNRS, ERL, Paris, France; INSERM, Unit U1201, Paris, France

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