CRISPRFinder protocols

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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 No

Documentation


Maintainer


This tool is not available anymore.

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 No

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Documentation


Maintainer


This tool is not available anymore.

Additional information


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

Publications for CRISPRFinder

CRISPRFinder in pipelines

 (106)
2018
PMCID: 5799301
PMID: 29403020
DOI: 10.1038/s41598-018-20889-x

[…] aligned using clustalw, and upgma tree representations of gene similarity were generated in the geneious software package (biomatters v.10.0.8). crispr spacer regions were detected using the crisprfinder software package, and repeats were enumerated per speices using custom-written scripts in matlab r2016b., assembled draft genomes were deposited to ncbi with accession numbers […]

2018
PMCID: 5807354
PMID: 29426864
DOI: 10.1038/s41598-018-20843-x

[…] (ecg28), ers1456455 (aiec01), ers1456456 (ecg11), ers1456457 (aiec07) and ers1456458 (ecg04)., mauve 2.3 was used to identify structural rearrangements and inversions throughout the strain’s genome. crisprfinder (http://crispr.i2bc.paris-saclay.fr/) was used to study crispr. to find gene content differences, blastp comparison (e-value cutoff 1e-5) and markov clustering (inflation factor 2.0) […]

2018
PMCID: 5908935
PMID: 29674546
DOI: 10.1128/genomeA.00277-18

[…] genes were identified by using resfinder version 2.1 (), virulence factors by using virulencefinder version 1.2 (), clustered regularly interspaced short palindromic repeat (crispr) arrays by using crisprfinder (), genomic islands by using islandviewer version 4 (), and prophage-related sequences by using phaster ()., the final assembly for shewanella sp. strain we21 resulted in one large […]

2017
PMCID: 5216340
PMID: 28057934
DOI: 10.1038/srep40206

[…] we removed prophages with a large number of insertion sequences (is; >25% of the predicted orfs). microsoft excel was used for all the statistical analysis., crispr array can be detected by crisprfinder. crispr arrays with two or more identical spacer lengths were identified. the graphical representations (logos) of the patterns in the alignments of all the consensus repeats of specific […]

2017
PMCID: 5267422
PMID: 28138357
DOI: 10.1186/s40793-017-0221-y

[…] in rps-blast against clusters of orthologous groups database and pfam database [–]. signalp was used to predict signal peptide [], and transmembrane helice was analyzed by tmhmm program []. crisprfinder was used for crispr identification []., the flammeovirga sp. sjp92 genome has only one circular chromosome of a total size of about 8, 534, 834 bp with a 34.80% gc content (containing […]


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CRISPRFinder in publications

 (335)
PMCID: 5944118
PMID: 29774086
DOI: 10.1186/s40793-018-0317-z

[…] (annotation software revision 4.1) ncbi prokaryotic genome annotation pipeline (annotation software revision 4.1) was used for gene calling and gene annotation. to identify crispr-cas sequences the crisprfinder server was used []. the pfam-a v29 database was used to predict pfam domains []. transmembrane domains were predicted with the webserver based tmhmm2 program [] and signal peptides […]

PMCID: 5944007
PMID: 29760866
DOI: 10.1186/s40793-018-0316-0

[…] were detected using blastclust with thresholds of 70% covered length and 30% sequence identity []. crispr, transmembrane helice, signalp and pfam protein families predictions were done using crisprfinder [], tmhmm server v.2.0 [], signalp 4.0 [] and pfam 29.0 [], respectively. the distribution of genes into cogs functional categories is presented in table .table 4table 5the total […]

PMCID: 5921776
PMID: 29725499
DOI: 10.1186/s40793-018-0315-1

[…] (iii) signal peptides were identified using the signalp server 4.1 [], and (iv) transmembrane helices were inferred using the tmhmm server v. 2.0 []. crispr repeats were identified using pgap and crisprfinder []., the properties of both draft genomes are summarized in table . the final assembly for strain ps6t consisted of 8 scaffolds, with a total length of 1,274,972 bp, and a g + c content […]

PMCID: 5912743
PMID: 29684056
DOI: 10.1371/journal.pone.0196290

[…] center for biotechnology information) prokaryotic genome automatic annotation pipeline (pgaap). for all other genomes, the published annotation from the ncbi genbank or refseq database was used. crisprfinder (http://crispr.i2bc.paris-saclay.fr/) was used to identify crispr (clustered regularly interspaced short palindromic repeats) within the genome sequences []. annotated genomes were also […]

PMCID: 5908935
PMID: 29674546
DOI: 10.1128/genomeA.00277-18

[…] genes were identified by using resfinder version 2.1 (), virulence factors by using virulencefinder version 1.2 (), clustered regularly interspaced short palindromic repeat (crispr) arrays by using crisprfinder (), genomic islands by using islandviewer version 4 (), and prophage-related sequences by using phaster ()., the final assembly for shewanella sp. strain we21 resulted in one large […]


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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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