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ProtospacerWB specifications

Information


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

Taxon


  • 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

Versioning


No version available

Documentation


Maintainer


Publication for Protospacer Workbench

ProtospacerWB citations

 (3)
library_books

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

2017
PMCID: 5365315
PMID: 28252384
DOI: 10.7554/eLife.23239.017

[…] 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, […]

library_books

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

2016
PMCID: 5172577
PMID: 27997583
DOI: 10.1371/journal.pone.0168362

[…] resulting in intermediate plasmids cm162 and cm163. a guide sgrna (sgrna2) sequence for pf230p was identified using the protospacer software (alpha version; https://sourceforge.net/projects/protospacerwb/files/release/) 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 […]

library_books

Minimizing off Target Mutagenesis Risks Caused by Programmable Nucleases

2015
PMCID: 4632775
PMID: 26501275
DOI: 10.3390/ijms161024751

[…] 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, […]


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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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