CRISPRDetect protocols

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CRISPRDetect specifications

Information


Unique identifier OMICS_12234
Name CRISPRDetect
Interface Web user interface
Restrictions to use None
Programming languages Perl
Computer skills Basic
Version 2.1
Stability Stable
Maintained Yes

Documentation


Maintainer


Information


Unique identifier OMICS_12234
Name CRISPRDetect
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 2.1
Stability Stable
Maintained Yes

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Documentation


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Publication for CRISPRDetect

CRISPRDetect in pipeline

2018
PMCID: 5883640
PMID: 29615108
DOI: 10.1186/s40168-018-0452-1

[…] covering more than 5% of the query were retained. whole genome dotplots were realized with gepard [], using a length of 11 nt for minimal exact matches. crispr spacers were searched for with crisprdetect [], using default parameters., for each prophage pair to be compared, all proteins of the first phage were compared to the proteins of the second one (blastp, e value < 10−3), […]


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CRISPRDetect in publications

 (8)
PMCID: 5764934
PMID: 29326210
DOI: 10.1128/genomeA.01405-17

[…] the motif vncggtgtannd (modified bases underlined)., the plasmid encodes a crispr-cas (clustered regularly interspaced short palindromic repeats and associated genes) system of the i-f type (). crisprdetect version 2.1 () identified a crispr array ranging from nucleotides 50488 to 45838 in reverse orientation on the plasmid and harboring 77 spacer sequences with a predominant length of 32 […]

PMCID: 5754499
PMID: 29301890
DOI: 10.1128/genomeA.01420-17

[…] islands; several putative insertion sequences and prophages were also detected. no clustered regularly interspaced short palindromic repeat (crispr) arrays were found after an inspection with crisprdetect ()., this whole-genome shotgun project has been deposited at ddbj/ena/genbank under the accession number nhml00000000. the version described in this paper is the first version, […]

PMCID: 5678084
PMID: 29118316
DOI: 10.1038/s41467-017-01449-9

[…] or human-associated lineages. the cas genes were identified by running hmmsearch (e-value < 1 × 10−5) against the cas hmm profiles retrieved from pfam. the crispr spacers were identified with crisprdetect., to evaluate the presence of adaptive signals governing the evolution of accessory genes we implemented two main approaches: (i) as described by andreani et al., the correlation […]

PMCID: 5608340
PMID: 28934361
DOI: 10.1371/journal.pone.0185234

[…] genomic coordinates) as described previously []. genomes were screened for the presence of clustered regularly interspaced short palindromic repeats (crisprs) using a combination of crisprfinder [], crisprdetect [], and crisprone (http://omics.informatics.indiana.edu/crisprone) while protospacer targets were analyzed using the crisprtarget [] server. transcriptional promoters and rho-independent […]

PMCID: 5541045
PMID: 28769116
DOI: 10.1038/s41598-017-07828-y

[…] was a crispr array in close proximity (less than 1 kb) to the rt gene identified. crispr array sites were identified and classified, and their orientation and properties were determined with the crisprdetect and crisprstrand algorithms. the correct orientation of the array was determined on the basis of the following criteria: (i) orientation predicted by the crispr-detect algorithm […]


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CRISPRDetect institution(s)
Department of Biochemistry, University of Otago, Dunedin, New Zealand; Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand; Genetics Otago, University of Otago, Dunedin, New Zealand

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