CRT statistics

Tool stats & trends

Looking to identify usage trends or leading experts?


CRT specifications


Unique identifier OMICS_03713
Name CRT
Alternative name CRISPR Recognition Tool
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input format FASTA
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Charles Bland

Publication for CRISPR Recognition Tool

CRT citations


Pan Genome Analysis Links the Hereditary Variation of Leptospirillum ferriphilum With Its Evolutionary Adaptation

Front Microbiol
PMCID: 5880901
PMID: 29636744
DOI: 10.3389/fmicb.2018.00577

[…] pplied for the computational identification of putative GIs. In addition, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci were identified using the web tool CRISPRFinder () or CRISPR Recognition Tool (). […]


Revisiting Francisella tularensis subsp. holarctica, Causative Agent of Tularemia in Germany With Bioinformatics: New Insights in Genome Structure, DNA Methylation and Comparative Phylogenetic Analysis

Front Microbiol
PMCID: 5859110
PMID: 29593661
DOI: 10.3389/fmicb.2018.00344

[…] aller than 500 bp and with less than 3 reads coverage) and Kraken testing.For genomic analysis the origin of replication (oriC) was identified using ori-Finder (). CRISPR loci were searched using the CRISPR Recognition Tool version 1.1 (). Prophage elements were searched by using PHAST (). Tandem repeats were searched for with a tandem repeat finder version 4.09 (). Average nucleotide identity (AN […]


Complete genome sequence of Lactobacillus rhamnosus Pen, a probiotic component of a medicine used in prevention of antibiotic associated diarrhoea in children

PMCID: 5822663
PMID: 29483943
DOI: 10.1186/s13099-018-0235-z

[…] of intrinsic antibiotic resistance among probiotic strains is valuable factor in restoring the intestinal microbiota after antibiotic treatment [].The analysis performed using CRISPRs finder and the Crispr Recognition Tool indicated that the genome contains one regularly interspaced short palindromic repeat locus consisting of a 1092-nt region with 16 spacers (30–31 nt in length) (Fig. ). The det […]


Genome of Russian wheat aphid an economically important cereal aphid

Stand Genomic Sci
PMCID: 5745598
PMID: 29299110
DOI: 10.1186/s40793-017-0307-6

[…] smaller than 10e-3 accepted as significant. Protein coding genes were analyzed for their amino acid content through use of the Geneious (v7.1.5) platform [] and CRISPR sites were predicted using the CRISPR Recognition Tool v1.1 [].Reads obtained from the SOLiD system were then mapped to the predicted protein coding genes of the SAM assembly to facilitate nucleotide variant calling using the Genei […]


Draft genome sequence of Venturia carpophila, the causal agent of peach scab

Stand Genomic Sci
PMCID: 5712196
PMID: 29213355
DOI: 10.1186/s40793-017-0280-0

[…] from Pfam [], SMART [], COG [], PRK [], and TIGRFAM []. The e-value for BLAST and RPSBLAST search in a database was 1e-50 and 0.01, respectively. In addition, CRISPR regions were identified using the CRISPR Recognition Tool (CRT) []; tRNAs were identified by tRNAScan-SE-1.23 []; rRNAs were identified by RNAmmer []; signal peptides and transmembrane helices were predicted using SignalP [] and TMHMM […]


Diversity of dsDNA Viruses in a South African Hot Spring Assessed by Metagenomics and Microscopy

PMCID: 5707555
PMID: 29156552
DOI: 10.3390/v9110348
call_split See protocol

[…] The CRISPR loci were searched in the curated read dataset, using Minced (, a metagenomic version of the CRISPR recognition tool (CRT) source code [], using the ‘minimum number of repeats to find” (minNR) to 3 and the rest set to defaults. To assign Brandvlei spacer regions to database isolates, the BHS […]


Looking to check out a full list of citations?

CRT institution(s)
Department of Computer Science, Jackson State University, Jackson, MS, USA; DOE Joint Genome Institute, Walnut Creek, CA, USA; Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA

CRT reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review CRT