CRISPR Visualizer: rapid identification and visualization of CRISPR loci via an automated high-throughput processing pipeline.
Matthew A NetheryRodolphe BarrangouPublished in: RNA biology (2018)
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.
Keyphrases
- genome wide
- high throughput
- crispr cas
- genome editing
- dna methylation
- copy number
- high resolution
- multiple sclerosis
- single cell
- gene expression
- genome wide association study
- electronic health record
- big data
- mass spectrometry
- cell free
- wastewater treatment
- image quality
- electron microscopy
- high density
- simultaneous determination
- sensitive detection
- amino acid
- clinical evaluation
- genome wide association