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CRISPRDetect specifications

Information


Unique identifier OMICS_12234
Name CRISPRDetect
Interface Web user interface
Restrictions to use None
Programming languages Perl
Computer skills Basic
Version 2.1
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Chris Brown

Information


Unique identifier OMICS_12234
Name CRISPRDetect
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 2.1
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Chris Brown

Publication for CRISPRDetect

CRISPRDetect citations

 (11)
library_books

Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes

2018
Microbiome
PMCID: 5883640
PMID: 29615108
DOI: 10.1186/s40168-018-0452-1

[…] ignments covering more than 5% of the query were retained. Whole genome dotplots were realized with Gepard [], using a length of 11 nt for minimal exact matches. CRISPR spacers were searched for with CRISPRDetect [], using default parameters. […]

library_books

Genomic repeats, misassembly and reannotation: a case study with long read resequencing of Porphyromonas gingivalis reference strains

2018
BMC Genomics
PMCID: 5771137
PMID: 29338683
DOI: 10.1186/s12864-017-4429-4

[…] poproteins.Insertion sequence transposases were renamed as per the ISfinder [] nomenclature. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) were identified using CRISPRfinder [], CRISPRDetect [], CRISPI [] webtools and the CRT plug-in [] with Geneious. We predicted genomic islands using IslandViewer (v4) [], which has precomputed predictions from SIGI-HMM [], IslandPath [], an […]

call_split

Complete Genome Sequencing of Acinetobacter sp. Strain LoGeW2 3, Isolated from the Pellet of a White Stork, Reveals a Novel Class D Beta Lactamase Gene

2018
Genome Announc
PMCID: 5764934
PMID: 29326210
DOI: 10.1128/genomeA.01405-17
call_split See protocol

[…] within the motif VNCGGTGTANND (modified bases underlined).The plasmid encodes a CRISPR-Cas (clustered regularly interspaced short palindromic repeats and associated genes) system of the I-F type (). CRISPRDetect version 2.1 () identified a CRISPR array ranging from nucleotides 50488 to 45838 in reverse orientation on the plasmid and harboring 77 spacer sequences with a predominant length of 32 nu […]

library_books

Draft Genome Sequence of Rhodococcus sp. Strain NCIMB 12038, a Naphthalene Degrading Bacterium

2018
Genome Announc
PMCID: 5754499
PMID: 29301890
DOI: 10.1128/genomeA.01420-17

[…] genomic islands; several putative insertion sequences and prophages were also detected. No clustered regularly interspaced short palindromic repeat (CRISPR) arrays were found after an inspection with CRISPRDetect (). […]

library_books

Distinct Campylobacter fetus lineages adapted as livestock pathogens and human pathobionts in the intestinal microbiota

2017
Nat Commun
PMCID: 5678084
PMID: 29118316
DOI: 10.1038/s41467-017-01449-9

[…] ociated or human-associated lineages. The Cas genes were identified by running hmmsearch (e-value < 1 × 10−5) against the Cas HMM profiles retrieved from Pfam. The CRISPR spacers were identified with CRISPRdetect. […]

library_books

Restriction modification mediated barriers to exogenous DNA uptake and incorporation employed by Prevotella intermedia

2017
PLoS One
PMCID: 5608340
PMID: 28934361
DOI: 10.1371/journal.pone.0185234

[…] s systems utilize multi-protein effector complexes, whereas class 2 CRISPR-Cas systems utilize single-protein effectors []. Analysis of ATCC-25611F and 17F genome sequences using a combination of the CRISPRdetect, CRISPROne and CRISPRfinder programs revealed two separate CRISPR systems present in both strains. The first system, located on chromosome I and designated CRISPR-I, has adjacent Cas prot […]

Citations

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CRISPRDetect institution(s)
Department of Biochemistry, University of Otago, Dunedin, New Zealand; Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand; Genetics Otago, University of Otago, Dunedin, New Zealand

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