CRT protocols

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


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  • person_outline Charles Bland <>

Publication for CRISPR Recognition Tool

CRT IN pipelines

PMCID: 5057446
PMID: 27777646
DOI: 10.1186/s40793-016-0198-y

[…] was based on homology searches using webmga [19]. rnammer 1.2 [20] and trnascan-se 1.4 [21] were used to identify rrna genes and trna genes, respectively. crispr repeats were examined using the crispr recognition tool [22]. signal peptides and transmembrane helices were predicted using signalp [23] and tmhmm [24], respectively., the assembly of the draft genome sequence comprises two […]

PMCID: 5630864
PMID: 27576538
DOI: 10.1093/gbe/evw203

[…] for phylogenetic analysis a neighbor-joining tree was constructed using mega6 (tamura et al. 2013) and tested with 1,000 bootstrap replications., crispr spacer arrays were predicted using the crispr recognition tool (bland et al. 2007) with the following setting: minimum repeats per array 3, repeat length 29–30 nt, spacer length 19–48 and search window 9 nt. a more inclusive crispr array […]

PMCID: 3914696
PMID: 24391155
DOI: 10.1093/gbe/evt209

[…] sequence analysis, technical university of denmark), respectively. the genome of atcc 700755t was visualized using dnaplotter (carver et al. 2009). crispr palindromic repeats were detected using crispr recognition tool (crt) (bland et al. 2007)., psychroflexus torquis atcc 700755t was grown on modified marine agar at different sea salt salinities and light intensities at 4 °c to examine […]

PMCID: 3409226
PMID: 22860008
DOI: 10.1371/journal.pone.0041706

[…] sequences were assembled using the dnastar lasergene software suite for sequence analysis version 7.2.0 (dnastar, inc.; madison, wi). crispr array spacer and repeat patterns were generated using the crispr recognition tool (crt) version 1.0 ( [37]. the repeat sequences within the crisprs 1, 2, and 3 were assessed for existing homology to known sequences using blast […]

PMCID: 3035220
PMID: 21304656
DOI: 10.4056/sigs.32535

[…] then all nonoverlapping domains are recorded. signal peptides were identified with signalp [30], and transmembrane helices were determined with tmhmm [31]. crispr elements were identified with the crispr recognition tool (crt) [32]. paralogs are hits of a protein against another protein within the same genome with an e-value of 10-2 or lower. more details about gene annotation procedures […]

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

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