CRISPRTarget protocols

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CRISPRTarget specifications

Information


Unique identifier OMICS_03712
Name CRISPRTarget
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for CRISPRTarget

CRISPRTarget in pipelines

 (2)
2016
PMCID: 5006608
PMID: 27577199
DOI: 10.1186/s12864-016-3040-4

[…] structure prediction of the repeats was performed using mfold (http://unafold.rna.albany.edu/?q=mfold/rna-folding-form) []. the spacers for each locus were manually identified and compared. crisprtarget (http://bioanalysis.otago.ac.nz/crisprtarget/crispr_analysis.html) [] was utilized to predict the presence of possible protospacers. protospacers were identified if the associated […]

2015
PMCID: 4607530
PMID: 26338188
DOI: 10.1093/gbe/evv174

[…] with the c. jejuni nctc 11168 and c. coli 76339 cas9 protein sequences using blast (basic local alignment search tool)., the 1,065 campylobacter crispr spacer alleles were used as query for the crisprtarget website (http://brownlabtools.otago.ac.nz/crisprtarget/crispr_analysis.html, last accessed september 8, 2015) (), and used to search the genbank-phage, refseq-plasmid, and refseq-viral […]


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CRISPRTarget in publications

 (33)
PMCID: 5704556
PMID: 29218031
DOI: 10.3389/fmicb.2017.02234

[…] clustered regularly interspaced short palindromic repeats (crispr) targets were identified by submitting the spacer sequences to analysis with the crispr target tool (http://bioanalysis.otago.ac.nz/crisprtarget) searching the genbank phage, refseq bacteria, refseq plasmid and refseq viral databases. we also searched the nucleotide collection (nr/nt) at ncbi using the default parameters, […]

PMCID: 5698299
PMID: 29162801
DOI: 10.1038/s41467-017-01591-4

[…] preferences for successful cleavage of a dna target. we used the 10 spacers of the g. thermodenitrificans t12 crispr locus to search for potential protospacers in viral and plasmid sequences using crisprtarget. as only two hits were obtained with phage genomes (supplementary fig. ), it was decided to proceed with an in vitro pam determination approach. the predicted sgrna sequence […]

PMCID: 5693588
PMID: 29177012
DOI: 10.1186/s13099-017-0215-8

[…] alignment (msa) using mega7 software []. the spacers of crispr were classified according to a phylogenetic tree inferred using mega7 software, and the spacer sequences were analyzed using the crisprtarget tool (http://bioanalysis.otago.ac.nz/crisprtarget/)., multiplex pcr was performed to detect h. pylori toxin genes, the caga gene, and the s and m regions of the vaca gene []. dna […]

PMCID: 5681539
PMID: 29127284
DOI: 10.1038/s41467-017-01408-4

[…] cas9 homologs and dna targets are often mutated in this region to escape cleavage by cas9. to identify the pam for geocas9, we first searched for naturally targeted viral and plasmid sequences using crisprtarget. the three sequenced strains of g. st. provided 77 spacer sequences, and 3 of them had high-confidence viral and plasmid targets (supplementary fig. , supplementary data ). extracting […]

PMCID: 5654357
PMID: 29097994
DOI: 10.3389/fmicb.2017.02036

[…] genes and additional signature genes (makarova et al., ). additionally, we investigated the possible targets (protospacers) of spacers in crispr-cas arrays within the obtained draft genomes using crisprtarget to search against all the available databases (i.e., genbank-phage, genbank-environmental, refseq-plasmid, refseq-viral, and refseq-bacteria), which was combined with the known features […]


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CRISPRTarget institution(s)
Department of Biochemistry; University of Otago; Dunedin, New Zealand; Laboratory of Microbiology; Wageningen University; Wageningen, Netherlands; Department of Microbiology and Immunology; University of Otago; Dunedin, New Zealand; Genetics Otago; University of Otago; New Zealand

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