CRISPRFinder statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

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 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

Download


download.png

Versioning


No version available

Documentation


Maintainer


This tool is not available anymore.

Additional information


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

Publications for CRISPRFinder

CRISPRFinder citations

 (395)
library_books

Complete genome sequence of “Thiodictyon syntrophicum” sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno

2018
Stand Genomic Sci
PMCID: 5944118
PMID: 29774086
DOI: 10.1186/s40793-018-0317-z

[…] Cad16T, four being located on the chromosome and one on the plasmid pTs485 (Fig. ). The number of DRs ranges from 19 (CRR4) to 146 (CRR2) as seen in Table .BLASTn analysis of the CRISPR DRsusing the CRISPRfinder platform revealed similarities in CRR1, CRR2 and CRR4 to sequences of “T. mobilis” 8321 (57 hits, 2 mismatches) and “Thioalkalivibrio sulfidophilus” HL-EbGr7 (63 hits, 3 mismatches). The […]

library_books

Short genome report of cellulose producing commensal Escherichia coli 1094

2018
Stand Genomic Sci
PMCID: 5944007
PMID: 29760866
DOI: 10.1186/s40793-018-0316-0

[…] clusters 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 . […]

library_books

High quality draft genome sequences of Mycoplasma agassizii strains PS6T and 723 isolated from Gopherus tortoises with upper respiratory tract disease

2018
Stand Genomic Sci
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 []. […]

library_books

Bifidobacteria isolated from vaginal and gut microbiomes are indistinguishable by comparative genomics

2018
PLoS One
PMCID: 5912743
PMID: 29684056
DOI: 10.1371/journal.pone.0196290

[…] onal 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 s […]

call_split

Complete Genome Sequence of Shewanella sp. WE21, a Rare Isolate with Multiple Novel Large Genomic Islands

2018
Genome Announc
PMCID: 5908935
PMID: 29674546
DOI: 10.1128/genomeA.00277-18
call_split See protocol

[…] e 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 closed c […]

library_books

Complete Genome Sequence of Spiroplasma floricola 23 6T (ATCC 29989), a Bacterium Isolated from a Tulip Tree (Liriodendron tulipifera L.)

2018
Genome Announc
PMCID: 5908944
PMID: 29674553
DOI: 10.1128/genomeA.00302-18

[…] obtain from the BlastKOALA tool () and BLASTP () searches against the NCBI nonredundant database (). Putative clustered regularly interspaced short palindromic repeats (CRISPRs) were identified using CRISPRFinder ().The complete genome sequence of Spiroplasma floricola 23-6T consists of one circular chromosome that is 1,284,130 bp in size with 24.3% G+C content; no plasmid was found. The first ver […]

Citations

Looking to check out a full list of citations?

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).

CRISPRFinder reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review CRISPRFinder