CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats

Abstract

Clustered regularly interspaced short palindromic repeat (CRISPR) elements are a particular family of tandem repeats present in prokaryotic genomes, in almost all archaea and in about half of bacteria, and which participate in a mechanism of acquired resistance against phages. They consist in a succession of direct repeats (DR) of 24–47 bp separated by similar sized unique sequences (spacers). In the large majority of cases, the direct repeats are highly conserved, while the number and nature of the spacers are often quite diverse, even among strains of a same species. Furthermore, the acquisition of new units (DR + spacer) was shown to happen almost exclusively on one side of the locus. Therefore, the CRISPR presents an interesting genetic marker for comparative and evolutionary analysis of closely related bacterial strains. CRISPRcompar is a web service created to assist biologists in the CRISPR typing process. Two tools facilitates the in silico investigation: CRISPRcomparison and CRISPRtionary. This website is freely accessible at http://crispr.u-psud.fr/CRISPRcompar/.

Emergence and Prevalence of Non-H 2 S-Producing Salmonella enterica Serovar Senftenberg Isolates Belonging to Novel Sequence Type 1751 in China

“…The PCR amplicons were sequenced by Sangon Biotech. Spacers were identified for CRISPR1 and CRISPR2 using CRISPRfinder (http://crispr .u-psud.fr/Server/) (23). Each spacer was queried using the Institut Pasteur CRISPR database for Salmonella (http://www.pasteur.fr/recherche /genopole/PF8/crispr/CRISPRDB.html) to obtain the spacer and direct repeat (DR) names.…”

New Clustered Regularly Interspaced Short Palindromic Repeat Locus Spacer Pair Typing Method Based on the Newly Incorporated Spacer for Salmonella enterica

“…All sequences from this study were submitted as a batch to a private database in CRISPRdb (http://crispr.u-psud.fr/CRISPRcompar/private /PrivateDatabase.php) under accession numbers 403_15795 to 403_15895. The analyses of the spacer arrangements were performed using CRISPRcompar (6). Different allelic types (ATs; sequences with at least a 1-nucleotide difference, or a 1-spacer difference in the case of CRISPRs) were assigned arbitrary numbers.…”

“…Restriction endonuclease digestion was carried out using XbaI (TaKaRa, Dalian, China) at 37°C for 3 h. DNA macrorestriction fragments were resolved on 1% SeaKem Gold agarose (Lonza, Rockland, ME, USA) using a CHEF Mapper PFGE system for over 19 h. S. enterica serovar Braenderup strain H9812 was used as the reference strain (16). BioNumerics version 6.0 was used to analyze the PFGE patterns. Similarity analysis was performed using the Dice coefficient, and clustering was performed using the unweighted-pair group method by arithmetic mean with a 1.5% tolerance limit.…”

“…The clustered regularly interspaced short palindromic repeat (CRISPR) that has been discovered in archaea and bacteria provides adaptive, heritable immunity against viruses, plasmids, and other mobile genetic elements (6). CRISPRs encode tandem sequences containing 21-to 47-bp direct repeats (DRs) and spacers of similar size.…”

Diversity, evolution, and therapeutic applications of small RNAs in prokaryotic and eukaryotic immune systems

“…In Archaea, CRISPR loci are more abundant. They also are generally more complex and longer [57,106]. The repeat sequences of Archaea and Bacteria are also quite different; there is not much overlap between the sequences of families of CRISPR loci from these two domains.…”