ArticleRNA biology2019
CRISPR Visualizer: rapid identification and visualization of CRISPR loci via an automated high-throughput processing pipeline.
Article in RNA biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
31 citing papers in PubMed.
- Genomic evidence of ecological flexibility and cross-niche CRISPR spacerome targeting phage-plasmid hybrids in Latilactobacillus curvatus.BMC genomics · 2026Article
- Comparative Genome Analysis and Characterization of Lacticaseibacillus Paracasei NKN344 Strain Isolated from Curd of Buffalo Milk Reared on Brackish Water Lagoons of the Eastern Indian Coast.Probiotics and antimicrobial proteins · 2026Article
- Enhanced editing ofApplied and environmental microbiology · 2026Article
- Characterization of diverse Cas9 orthologs for genome and epigenome editing.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Unlocking the potential of CRISPR tools and databases for precision genome editing.Frontiers in plant science · 2025Review
- Article
- CRISPR typing and phage content of colonizing Group BFrontiers in cellular and infection microbiology · 2025Article
- SpacerPlacer: ancestral reconstruction of CRISPR arrays reveals the evolutionary dynamics of spacer deletions.Nucleic acids research · 2024Article
- Genomic and phenotypic characterization ofMicrobial genomics · 2023Article
- CRISPR Comparison Toolkit: Rapid Identification, Visualization, and Analysis of CRISPR Array Diversity.The CRISPR journal · 2023Article
- Comparative genomics ofComputational and structural biotechnology journal · 2023Article
- Comparative Genomics of Lentilactobacillus parabuchneri isolated from dairy, KEM complex, Makgeolli, and Saliva Microbiomes.BMC genomics · 2022Article
- Comparative genomics of Leuconostoc lactis strains isolated from human gastrointestinal system and fermented foods microbiomes.BMC genomic data · 2022Article
- CrisprVi: a software for visualizing and analyzing CRISPR sequences of prokaryotes.BMC bioinformatics · 2022Article
- Salmonella enterica Serovar Typhimurium Isolates from Wild Birds in the United States Represent Distinct Lineages Defined by Bird Type.Applied and environmental microbiology · 2022Article
- Evidence for common ancestry and microevolution of passerine-adaptedMicrobial genomics · 2022Article
- Clustered Regularly Interspaced Short Palindromic Repeats Genotyping of Multidrug-ResistantFrontiers in microbiology · 2022Article
- Analyzing the genetic diversity and biotechnological potential ofFrontiers in microbiology · 2022Article
- CRISPRclassify: Repeat-Based Classification of CRISPR Loci.The CRISPR journal · 2021Article
- Diversity of the type I-U CRISPR-Cas system in Bifidobacterium.Archives of microbiology · 2021Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A CRISPR locus, defined by an array of repeat and spacer elements, constitutes a genetic record of the ceaseless battle between bacteria and viruses, showcasing the genomic integration of spacers acquired from invasive DNA. In particular, iterative spacer acquisitions represent unique evolutionary histories and are often useful for high-resolution bacterial genotyping, including comparative analysis of closely related organisms, clonal lineages, and clinical isolates. Current spacer visualization methods are typically tedious and can require manual data manipulation and curation, including spacer extraction at each CRISPR locus from genomes of interest. Here, we constructed a high-throughput extraction pipeline coupled with a local web-based visualization tool which enables CRISPR spacer and repeat extraction, rapid visualization, graphical comparison, and progressive multiple sequence alignment. We present the bioinformatic pipeline and investigate the loci of reference CRISPR-Cas systems and model organisms in 4 well-characterized subtypes. We illustrate how this analysis uncovers the evolutionary tracks and homology shared between various organisms through visual comparison of CRISPR spacers and repeats, driven through progressive alignments. Due to the ability to process unannotated genome files with minimal preparation and curation, this pipeline can be implemented promptly. Overall, this efficient high-throughput solution supports accelerated analysis of genomic data sets and enables and expedites genotyping efforts based on CRISPR loci.
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