CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats

By Ibtissem Grissa, Gilles Vergnaud, Christine Pourcel. Nucleic Acids Res., 2007

1,886 citations recorded by the source corpus.

Clustered regularly interspaced short palindromic repeats (CRISPRs) constitute a particular family of tandem repeats found in a wide range of prokaryotic genomes (half of eubacteria and almost all archaea). They consist of a succession of highly conserved regions (DR) varying in size from 23 to 47 bp, separated by similarly sized unique sequences (spacer) of usually viral origin. A CRISPR cluster is flanked on one side by an AT-rich sequence called the leader and assumed to be a transcriptional promoter. Recent studies suggest that this structure represents a putative RNA-interference-based immune system. Here we describe CRISPRFinder, a web service offering tools to (i) detect CRISPRs including the shortest ones (one or two motifs); (ii) define DRs and extract spacers; (iii) get the flanking sequences to determine the leader; (iv) blast spacers against Genbank database and (v) check if the DR is found elsewhere in prokaryotic sequenced genomes. CRISPRFinder is freely accessible at http://crispr.u-psud.fr/Server/CRISPRfinder.php.

Subfields: Ecology, Epidemiology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9a35375787e6bc880d9893565120f41cba8c9fac

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology

In Epidemiology

In Molecular Biology

Citations in the corpus

Transcriptome engineering with RNA-targeting Type VI-D CRISPR effectors (2018, positive): “G Laboratory of Didier Trono Addgene #12259 EF1a-PspCas13b-NES(HIV)-2A-EGFP This paper Adapted from Addgene #103862 from Feng Zhang pC0043-PspCas13b crRNA backbone Cox et al., 2017 Addgene #103854 pC016-LwCas13a guide expression backbone with U6 promoter Abudayyeh et al., 2017 Addgene #91906 EF1a-Lw”
Metagenomics - a guide from sampling to data analysis (2012, background): “There exists also a number of tools for the prediction of non-protein coding genes such as tRNAs [66,67], signal peptides [68] or CRISPRs [69,70], however they might require significant computational resources or long contiguous sequences.”
Propionibacterium acnes strain populations in the human skin microbiome associated with acne (2013, methodology): “CRISPRFinder (Grissa et al., 2007) was used to identify the CRISPR repeat-spacer sequences.”
Discovery and functional characterization of diverse Class 2 CRISPR-Cas systems (2015, methodology): “CRISPR repeats were identified using PILER-CR (Edgar, 2007) or, for degenerate repeats, CRISPRfinder (Grissa et al., 2007).”
CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins (2018, background): “(7) and the differences are listed in Supplementary Material.”
MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems (2014, background): “Tools are available to detect and analyse CRISPR arrays [17–19], however, no program is available to detect and class cas operons themselves.”
CRISPRTarget (2013, methodology): “52 These spacers are used for a BLAST search of the nucleotide sequence database from GenBank using the default parameters.”
Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. (2015, neutral): “CRISPR repeats were identified using PILER-CR (Edgar, 2007) and CRISPRfinder (Grissa et al., 2007).”
Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions (2012, methodology): “CRISPRs identified using the CRISPRFinder program [55] are”
CRISPRDetect: A flexible algorithm to define CRISPR arrays (2016, methodology): “Then, to facilitate CRISPR prediction and analysis, a number of tools were developed, including both command-line executable programs (e.g. CRT [13], MINCED [14] and PILER-CR [15]) and web-applications (e.g. CRISPRFinder, CRISPI) [16, 17].”
CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. (2011, background): “Among different species, the length of the repeat can vary from 21 bp to 48 bp, whereas spacers are typically between 26 bp and 72 bp (33, 35).”
RNA-guided genetic silencing systems in bacteria and archaea (2012, background): “Architecture and composition of CRISPR loci The defining feature of CRISPR loci is a series of direct repeats (approximately 20–50 base pairs) separated by unique spacer sequences of a similar lengt”
Diversity, Activity, and Evolution of CRISPR Loci in Streptococcus thermophilus (2007, methodology): “Several sequences were retrieved from the CRISPRdb database (9) or found by using CRISPRFinder (10).”