CRISPRFinder protocols

CRISPRFinder specifications

Information


Unique identifier OMICS_03715
Name CRISPRFinder
Alternative name CRISPRCasFinder
Interface Web user interface
Restrictions to use None
Input data Some DNA sequences.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Christine Pourcel <>

Additional information


http://crispr.i2bc.paris-saclay.fr/

Information


Unique identifier OMICS_03715
Name CRISPRFinder
Alternative name CRISPRCasFinder
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some DNA sequences.
Input format FASTA
Operating system Unix/Linux, Mac OS
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


Add your version

Documentation


Maintainer


  • person_outline Christine Pourcel <>

Additional information


http://crispr.i2bc.paris-saclay.fr/

Publications for CRISPRFinder

CRISPRFinder IN pipelines

 (21)
2018
PMCID: 5767232
PMID: 29375506
DOI: 10.3389/fmicb.2017.02637

[…] according to their predicted function, which included nitrogen metabolism, carbon fixation, respiration, and motility (supplementary data sheet s2). crispr repeat sequences were identified using crisprfinder (grissa et al., 2007)., the average nucleotide identity (ani) and the average amino acid identity (aai) among nitrospira genome sequences were calculated using online tools (rodriguez-r […]

2017
PMCID: 5289962
PMID: 28217118
DOI: 10.3389/fmicb.2017.00132

[…] using kegg databases (kanehisa and goto, 2000) and the functional comparative comparison tool found in the seed viewer (overbeek et al., 2014). crispr sequences and spacers were identified using the crisprfinder tool (grissa et al., 2007)., compositional analysis of leuconostoc in five commercially available starter cultures was performed in triplicates on total dna isolated from the starter […]

2017
PMCID: 5383892
PMID: 28385844
DOI: 10.1128/genomeA.00125-17

[…] values ranging from 73% to 94%. the analysis of the genome sequences for the presence of clustered regularly interspaced short palindromic repeat (crispr)–crispr-associated (cas) systems (9) with crisprfinder (10) confirmed the presence of a crispr-cas region in strain ccug 7206 and one region in strain ccug 35272 formed by one array of spacer repeats that contained five spacers in ccug 7206 […]

2017
PMCID: 5454432
PMID: 28534836
DOI: 10.3390/v9050120

[…] all published s. islandicus genomes and contigs from unpublished draft genomes from three yellowstone national park s. islandicus strains (y08.82.36, nl13.c01.02, nl01.b.c01.24) were extracted using crisprfinder [52] and oriented based on the repeat sequence flanking the spacer. in-house software (cldb v0.2, a computational toolset for comprehensively analyzing crispr locus diversity […]

2017
PMCID: 5561391
PMID: 28861046
DOI: 10.3389/fmicb.2017.01483

[…] resistance database (mcarthur et al., 2013). prophage prediction was done with phast (zhou et al., 2011) and clustered regularly interspaced short palindromic repeats (crispr) were predicted by crisprfinder (grissa et al., 2007). for genome similarity assessment, average nucleotide identity (ani) was computed using edgar 2.0 (blom et al., 2016)., the pan genome, core genome, and specific […]

CRISPRFinder institution(s)
Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Universite Paris-Saclay, Gif-sur-Yvette, France; Microbial Evolutionary Genomics, Institut Pasteur, Paris, France; CNRS, UMR3525, Paris, France; Universite Lille 1, CRIStAL, equipe Bonsai, Villeneuve d’Ascq, France; Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS - Paris, Institut Pasteur, Paris, France
CRISPRFinder funding source(s)
Supported by Institut Français de Bioinformatique (IFB) [ANR-11- INSB-0013, in part]; European Defense Agency Research and Technology project JIP-ICET2 A-1341-RT-GP, called Bioforensics for Biodefence (B2-forensics).

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