CRISPRFinder specifications

Information


Unique identifier OMICS_03715
Name CRISPRFinder
Interface Web user interface
Restrictions to use None
Input data DNA sequence(s)
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Archaebacteria
  • Eubacteria

CRISPRFinder article

CRISPRFinder citations

 (8)
2018
PMCID: 5908935

[…] were identified by using resfinder version 2.1 (9), virulence factors by using virulencefinder version 1.2 (10), clustered regularly interspaced short palindromic repeat (crispr) arrays by using crisprfinder (11), genomic islands by using islandviewer version 4 (12), and prophage-related sequences by using phaster (13)., the final assembly for shewanella sp. strain we21 resulted in one large […]

2017
PMCID: 5747140

[…] of strain jl1095t were predicted using rrnammer software [23], trna genes were identified using trnascan-se [24], and srna were predicted by blast searches against the rfam database [25]. the online crisprfinder program was used for crispr identification [26]., the 10.1601/nm.26592 jl1095t genome was composed of 5,043,263 bp with a g + c content of 68.63%. a total of 4286 protein-coding genes […]

2017
PMCID: 5631455

[…] connecticut department of public health (n = 115). whole genome sequencing was performed and genes for o-antigen (serotype), multilocus sequence typing (mlst) and virulence factors were extracted. crisprfinder and geneious were used for crispr loci., a phylogenetic tree based on mlst found no geographic clustering of the strains. similarly, no difference was observed for stx1 (mi: 89.6%, ct: […]

2015
PMCID: 4521832

[…] including the non-coding tracrrna and target pam sequence, for select systems., the genomes used were previously described by milani et al. [19] (table 1). crispr analyses were performed using crisprfinder followed by manual curation to identify and assemble repeat-spacer arrays [32]. blast [33] was used to identify cas proteins and confirm subtype designation [13]. snapgene (gsl biotech) […]

2015
PMCID: 4392142

[…] were found in genome, respectively. in addition, 16 genomic islands (gis) and 22 clustered regularly interspaced short palindromic repeats (crispr) were predicted using islandpath-diomb software and crisprfinder (http://crispr.u-psud.fr/), respectively., this whole-genome shotgun project has been deposited at ddbj/embl/genbank under the accession number jxsx00000000. the version described […]

CRISPRFinder institution(s)
Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France; Centre d’Etude du Bouchet, Vert le Petit, France
CRISPRFinder funding source(s)
The CNRS and Université Paris Sud 11 have funded this project.

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