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The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats

Grissa, Ibtissem, Vergnaud, Gilles, Pourcel, Christine·2007·BMC Bioinformatics
DOI 10.1186/1471-2105-8-172PMC PMC1892036
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Abstract

Background: In Archeae and Bacteria, the repeated elements called CRISPRs for "clustered regularly interspaced short palindromic repeats" are believed to participate in the defence against viruses. Short sequences called spacers are stored in-between repeated elements. In the current model, motifs comprising spacers and repeats may target an invading DNA and lead to its degradation through a proposed mechanism similar to RNA interference. Analysis of intra-species polymorphism shows that new motifs (one spacer and one repeated element) are added in a polarised fashion. Although their principal characteristics have been described, a lot remains to be discovered on the way CRISPRs are created and evolve. As new genome sequences become available it appears necessary to develop automated scanning tools to make available CRISPRs related information and to facilitate additional investigations. Description: We have produced a program, CRISPRFinder, which identifies CRISPRs and extracts the repeated and unique sequences. Using this software, a database is constructed which is automatically updated monthly from newly released genome sequences. Additional tools were created to allow the alignment of flanking sequences in search for similarities between different loci and to build dictionaries of unique sequences. To date, almost six hundred CRISPRs have been identified in 475 published genomes. Two Archeae out of thirty-seven and about half of Bacteria do not possess a CRISPR. Fine analysis of repeated sequences strongly supports the current view that new motifs are added at one end of the CRISPR adjacent to the putative promoter. Conclusion: It is hoped that availability of a public database, regularly updated and which can be queried on the web will help in further dissecting and understanding CRISPR structure and flanking sequences evolution. Subsequent analyses of the intra-species CRISPR polymorphism will be facilitated by CRISPRFinder and the dictionary creator. CRISPRdb is accessible at http://crispr.u-psud.fr/crispr

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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 [8]

    The Background (page unavailable) says CRISPRs occur in the majority of Archaea and many Bacteria and notes their presence on megaplasmids. The Abstract’s Description (page unavailable) reports CRISPRs in 35 of 37 Archaea (about 95%) and about half of Bacteria, not the claimed ~87% and ~45%; it gives no prevalence estimate for plasmids. (LLM, conf=0.87)

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  • The number of spacers within a CRISPR array can range from as few as one to several hundred, depending on the species.

    “The number of spacers within a CRISPR array can range from as few as one to several hundred, depending on the species [8].”

    From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [8]

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Citations

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Research works printed but not linked: 23

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Metadata

Authors
Grissa, I., Vergnaud, G., & Pourcel, C.
Venue
BMC Bioinformatics
Publisher
Springer Science and Business Media LLC
Published
2007-05-23
Volume
8
Issue
1
ISSN
1471-2105
DOI
10.1186/1471-2105-8-172
PMC
PMC1892036
Cited by
888
References
1
Language
en

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