ArticleThe CRISPR journal2023
CRISPR Comparison Toolkit: Rapid Identification, Visualization, and Analysis of CRISPR Array Diversity.
Article in The CRISPR journal, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 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
15 citing papers in PubMed, 18 citations in OpenAlex.
- CRISPR-Cas immune repertoires as an ecological record of bacterial interactions with mobile genetic elements in the human gut.Gut microbes · 2026Article
- Exploring the emerging role of CRISPR-Cas systems in probiotic development.Engineering microbiology · 2026Review
- Whole genome sequence-based comparative genomics reveals preliminary genomic features of Salmonella enterica subsp. enterica serovar Enteritidis phage type 1 and phage type 4 strains from EnteroBase.BMC microbiology · 2026Article
- Expanding the Microbial Genomic Landscape and Biotechnological Applications of CRISPR-Cas Systems.Biology · 2026Review
- An evolutionary approach to predict the orientation of CRISPR arrays.PLoS computational biology · 2025Article
- Emergence of transmissibleApplied and environmental microbiology · 2025Article
- Mobile gene clusters and coexpressed plant-rhizobium pathways drive partner quality variation in symbiosis.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Exploring sub-species variation in food microbiomes: a roadmap to reveal hidden diversity and functional potential.Applied and environmental microbiology · 2025Review
- Evolutionary responses of Escherichia coli to phage pressure: insights into mucoidy and colanic acid overexpression.BMC genomics · 2025Article
- Metagenomic CRISPR Array Analysis Tool: a novel graph-based approach to finding CRISPR arrays in metagenomic datasets.microLife · 2025Article
- SpacerPlacer: ancestral reconstruction of CRISPR arrays reveals the evolutionary dynamics of spacer deletions.Nucleic acids research · 2024Article
- Article
- Kinetic, genomic, and physiological analysis reveals diversity in the ecological adaptation and metabolic potential ofMicrobiology spectrum · 2023Article
- Horizontal Gene Transfer and CRISPR Targeting Drive Phage-Bacterial Host Interactions and Coevolution in "Pink Berry" Marine Microbial Aggregates.Applied and environmental microbiology · 2023Article
- Draft genome sequence of Enterobacter chengduensis ECC445, isolated from fresh water in the West Indies.BMC genomic data · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
CRISPR-Cas systems provide immunity against mobile genetic elements (MGEs) through sequence-specific targeting by spacer sequences encoded in CRISPR arrays. Spacers are highly variable between microbial strains and can be acquired rapidly, making them well suited for use in strain typing of closely related organisms. However, no tools are currently available to automate the process of reconstructing strain histories using CRISPR spacers. We therefore developed the CRISPR Comparison Toolkit (CCTK) to enable analyses of array relationships. The CCTK includes tools to identify arrays, analyze relationships between arrays using CRISPRdiff and CRISPRtree, and predict targets of spacers. CRISPRdiff visualizes arrays and highlights the similarities between them. CRISPRtree infers a phylogenetic tree from array relationships and presents a hypothesis of the evolutionary history of the arrays. The CCTK unifies several CRISPR analysis tools into a single command line application, including the first tool to infer phylogenies from array relationships.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.