ArticleBMC bioinformatics2017
Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers.
What it found
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Who cites it
106 citing papers in PubMed, 199 citations in OpenAlex.
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- The complexity of multiple CRISPR arrays in strains with (co-occurring) CRISPR systems.microLife · 2026Article
- Characterization and diversity of defense systems inFrontiers in immunology · 2026Article
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- Functional genomics of a food-related thermotolerant Acetobacter oryzifermentans strain AAB5: genetic determinants of stress response, CAZyme repertoire, and CRISPR-Cas system.Functional & integrative genomics · 2025Article
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- In silico approaches for discovering microbial antiviral defense systems.Briefings in bioinformatics · 2025Review
- CRISPR-GATE: a one-stop repository and guide to computational resources for genome editing experimentation.Briefings in bioinformatics · 2025Review
- Whole-genome sequencing and probiotic properties of Lactobacillus helveticus KM7 isolated from the gut of the Chinese honey bee (Apis cerana): A promising exopolysaccharide-producing strain.BMC microbiology · 2025Article
- Comparative Genomic Analysis and Antimicrobial Resistance Profile ofVeterinary sciences · 2025Article
- Evolutionary trends inmSystems · 2025Article
- Rapid whole genome sequencing for AMR surveillance in low- and middle-income countries: Oxford Nanopore Technology reveals multidrug-resistant Enterobacter cloacae complex from dairy farms in Sri Lanka.BMC veterinary research · 2025Article
- CRISPR-Cas9 and Its Bioinformatics Tools: A Systematic Review.Current issues in molecular biology · 2025Review
- Genome Mining and Characterization of Two NovelBiomolecules · 2025Article
- Metagenomic characterization of the metabolism, evolution, and global distribution of Candidatus Accumulibacter members in wastewater treatment plants.The ISME journal · 2025Article
- Unlocking the potential of CRISPR tools and databases for precision genome editing.Frontiers in plant science · 2025Review
- CRISPR-Cas System, Antimicrobial Resistance, andBiomedicines · 2024Article
- Phylogenomic and genomic analysis reveals unique and shared genetic signatures ofMicrobial genomics · 2024Article
- Genomic characterization and probiotic potential assessment of an exopolysaccharide-producing strain Pediococcus pentosaceus LL-07 isolated from fermented meat.BMC microbiology · 2024Article
46 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
backgroundThe CRISPR-Cas systems in prokaryotes are RNA-guided immune systems that target and deactivate foreign nucleic acids. A typical CRISPR-Cas system consists of a CRISPR array of repeat and spacer units, and a locus of cas genes. The CRISPR and the cas locus are often located next to each other in the genomes. However, there is no quantitative estimate of the co-location. In addition, ad-hoc studies have shown that some non-CRISPR genomic elements contain repeat-spacer-like structures and are mistaken as CRISPRs.
resultsUsing available genome sequences, we observed that a significant number of genomes have isolated cas loci and/or CRISPRs. We found that 11%, 22% and 28% of the type I, II and III cas loci are isolated (without CRISPRs in the same genomes at all or with CRISPRs distant in the genomes), respectively. We identified a large number of genomic elements that superficially reassemble CRISPRs but don't contain diverse spacers and have no companion cas genes. We called these elements false-CRISPRs and further classified them into groups, including tandem repeats and Staphylococcus aureus repeat (STAR)-like elements.
conclusionThis is the first systematic study to collect and characterize false-CRISPR elements. We demonstrated that false-CRISPRs could be used to reduce the false annotation of CRISPRs, therefore showing them to be useful for improving the annotation of CRISPR-Cas systems.
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