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CRISPI: a CRISPR interactive database

Rousseau, Christine, Gonnet, Mathieu, Le Romancer, Marc, Nicolas, Jacques·2009·Bioinformatics
DOI 10.1093/bioinformatics/btp586PMC PMC2788928
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Abstract

Summary: The CRISPR genomic structures (Clustered Regularly Interspaced Short Palindromic Repeats) form a family of repeats that is largely present in archaea and frequent in bacteria. On the basis of a formal model of CRISPR using very few parameters, a systematic study of all their occurrences in all available genomes of Archaea and Bacteria has been carried out. This has resulted in a relational database, CRISPI, which also includes a complete repertory of associated CRISPR-associated genes (CAS). A user-friendly web interface with many graphical tools and functions allows users to extract results, find CRISPR in personal sequences or calculate sequence similarity with spacers. Availability: CRISPI free access at http://crispi.genouest.org Contact: croussea@irisa.fr; jnicolas@irisa.fr;

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Crossref · 10.1093/bioinformatics/btp586

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  • Bioinformatic databases predict that CRISPR systems are prevalent in Archaea (~87%) and can be found on many bacterial genomes and plasmids (~45%).

    “Bioinformatic databases (CRISPRdb and CRISPI) dedicated to finding CRISPR motifs and Cas proteins on sequenced genomes predict that these systems are prevalent in Archaea (~87%) and can be found on many bacterial genomes and plasmids (~45%) [8,9].”

    From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [9]

    The Introduction (page unavailable) says CRISPRs occur in all but six archaeal species and half of bacteria, broadly supporting their prevalence. The paper does not give the cited 87% or 45% figures or report CRISPR systems on plasmids; it mentions plasmids only as possible sources of spacer material. (LLM, conf=0.88)

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Research works printed but not linked: 10

  1. Barrangou, 2007, CRISPR provides acquired resistance against viruses in prokaryotes, Science, 315, 1709, 10.1126/science.1138140 · DOI · Paper page
  2. Bland, 2007, CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats, BMC Bioinformatics, 8, 209, 10.1186/1471-2105-8-209 · DOI
  3. Durand, 2006, Browsing repeats in genomes: Pygram and an application to non-coding region analysis, BMC Bioinformatics, 7, 477, 10.1186/1471-2105-7-477 · DOI
  4. Edgar, 2007, Piler-cr: fast and accurate identification of crispr repeats, BMC Bioinformatics, 8, 18, 10.1186/1471-2105-8-18 · DOI
  5. Grissa, 2007, The crisprdb database and tools to display crisprs and to generate dictionaries of spacers and repeats, BMC Bioinformatics, 8, 172, 10.1186/1471-2105-8-172 · DOI · Paper page
  6. Grissa, 2007, CRISPRfinder: a web tool to identify clustered regularly interspaced short palindromic repeats, Nucleic Acids Res., 35, W52, 10.1093/nar/gkm360 · DOI
  7. Kunin, 2007, Evolutionary conservation of sequence and secondary structures in crispr repeats, Genome Biol., 8, R61, 10.1186/gb-2007-8-4-r61 · DOI
  8. Nicolas, 2008, Modeling local repeats on genomic sequences
  9. Sorek, 2008, CRISPR - a widespread system that provides acquired resistance against phages in bacteria and archaea, Nat. Rev. Microbiol., 6, 181, 10.1038/nrmicro1793 · DOI
  10. Stothard, 2005, Circular genome visualization and exploration using cgview, Bioinformatics, 21, 537, 10.1093/bioinformatics/bti054 · DOI

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Metadata

Authors
Rousseau, C., Gonnet, M., Le Romancer, M., & Nicolas, J.
Affiliations
1 IRISA-INRIA, Campus de Beaulieu, 35042 Rennes cedex and 2UMR 6197 Microbiologie des environnements extrêmes, technopôle Brest-Iroise, BP 70 29280 Plouzané, France
Venue
Bioinformatics
Publisher
Oxford University Press (OUP)
Published
2009-10-21
Volume
25
Issue
24
Pages
3317-3318
ISSN
  • 1367-4811
  • 1367-4803
DOI
10.1093/bioinformatics/btp586
PMC
PMC2788928
Cited by
110
References
0
Language
en
Licence
creativecommons.org/licenses/by-nc/2.0/uk/ (vor, 2538 d)

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