ArticleBMC genomics2016
CRISPRDetect: A flexible algorithm to define CRISPR arrays.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 191 papers, 2 of them syntheses that pooled it.
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Who cites it
191 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Transitioning from wet lab to artificial intelligence: a systematic review of AI predictors in CRISPR.Journal of translational medicine · 2025Pooled it
- Advances in phage-host interaction prediction: in silico method enhances the development of phage therapies.Briefings in bioinformatics · 2024Pooled it
- Phage bioinformatics tools: a review of computational approaches for bacteriophage research.Briefings in bioinformatics · 2026Review
- Three novel Rothia species associated with Antarctic birds harbour novel biosynthetic gene clusters.FEMS microbiology ecology · 2026Article
- Deciphering the pangenome of the shellfish pathogenMicrobial genomics · 2026Article
- Characterisation and In Planta Activity of Bacteriophages That Infect the Key Bacterial Species Associated With Acute Oak Decline.Microbial biotechnology · 2026Article
- Understanding the probiotic potential of a healthy human vaginal flora, Lactobacillus gasseri K9: genomic and in vitro aspects.Journal, genetic engineering & biotechnology · 2026Article
- Defense Systems and Prophage Detection in Streptococcus mutans Strains.Molecular oral microbiology · 2026Article
- Application and Research Prospects of CRISPR/Cas Gene Editing Technology in Lactic Acid Bacteria.Microorganisms · 2026Review
- Viral communities from long-term anaerobic alkane-oxidizing enrichment cultures encode predicted cell surface adhesion functions.The ISME journal · 2026Article
- Identification and characterization of a novel plaque-invisible lytic single-stranded RNA phage.Journal of virology · 2025Article
- Genomic and functional characterization of a novel temperate Coventryvirus phage infecting Staphylococcus pseudintermedius.Scientific reports · 2025Article
- Advancing CRISPR with deep learning: A comprehensive review of models and databases.Molecular therapy. Nucleic acids · 2025Review
- Structures reveal how the Cas1-2/3 integrase captures, delivers, and integrates foreign DNA into CRISPR loci.Structure (London, England : 1993) · 2025Article
- An evolutionary approach to predict the orientation of CRISPR arrays.PLoS computational biology · 2025Article
- Whole-genome analysis ofMicrobiology spectrum · 2025Article
- A Phylogenetic Host-Range Index Reveals Ecological Constraints in Phage Specialisation and Virulence.Molecular ecology · 2025Article
- CRISPR-GATE: a one-stop repository and guide to computational resources for genome editing experimentation.Briefings in bioinformatics · 2025Review
- Comprehensive in vitro and whole-genome characterization of probiotic properties in Pediococcus acidilactici P10 isolated from Iranian broiler chicken.Scientific reports · 2025Article
- Multi-kingdom microbiota analysis reveals bacteria-viral interplay in IBS with depression and anxiety.NPJ biofilms and microbiomes · 2025Article
131 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCRISPR (clustered regularly interspaced short palindromic repeats) RNAs provide the specificity for noncoding RNA-guided adaptive immune defence systems in prokaryotes. CRISPR arrays consist of repeat sequences separated by specific spacer sequences. CRISPR arrays have previously been identified in a large proportion of prokaryotic genomes. However, currently available detection algorithms do not utilise recently discovered features regarding CRISPR loci.
resultsWe have developed a new approach to automatically detect, predict and interactively refine CRISPR arrays. It is available as a web program and command line from bioanalysis.otago.ac.nz/CRISPRDetect. CRISPRDetect discovers putative arrays, extends the array by detecting additional variant repeats, corrects the direction of arrays, refines the repeat/spacer boundaries, and annotates different types of sequence variations (e.g. insertion/deletion) in near identical repeats. Due to these features, CRISPRDetect has significant advantages when compared to existing identification tools. As well as further support for small medium and large repeats, CRISPRDetect identified a class of arrays with 'extra-large' repeats in bacteria (repeats 44-50 nt). The CRISPRDetect output is integrated with other analysis tools. Notably, the predicted spacers can be directly utilised by CRISPRTarget to predict targets.
conclusionCRISPRDetect enables more accurate detection of arrays and spacers and its gff output is suitable for inclusion in genome annotation pipelines and visualisation. It has been used to analyse all complete bacterial and archaeal reference genomes.
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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.