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Viruses 2018, 10(11), 602; https://doi.org/10.3390/v10110602

CRISPRStudio: A User-Friendly Software for Rapid CRISPR Array Visualization

1
Département de Biochimie, de Microbiologie, et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada
2
Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec City, QC G1V 0A6, Canada
3
SyntBioLab Inc., 4820 rue de la Pascaline, Lévis, QC G6W 0L9, Canada
4
COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
*
Author to whom correspondence should be addressed.
Received: 10 October 2018 / Revised: 29 October 2018 / Accepted: 30 October 2018 / Published: 1 November 2018
(This article belongs to the Special Issue Applications of CRISPR Technology in Virology 2018)
Full-Text   |   PDF [3613 KB, uploaded 1 November 2018]   |  

Abstract

The CRISPR-Cas system biologically serves as an adaptive defense mechanism against phages. However, there is growing interest in exploiting the hypervariable nature of the CRISPR locus, often of viral origin, for microbial typing and tracking. Moreover, the spacer content of any given strain provides a phage resistance profile. Large-scale CRISPR typing studies require an efficient method for showcasing CRISPR array similarities across multiple isolates. Historically, CRISPR arrays found in microbes have been represented by colored shapes based on nucleotide sequence identity and, while this approach is now routinely used, only scarce computational resources are available to automate the process, making it very time-consuming for large datasets. To alleviate this tedious task, we introduce CRISPRStudio, a command-line tool developed to accelerate CRISPR analysis and standardize the preparation of CRISPR array figures. It first compares nucleotide spacer sequences present in a dataset and then clusters them based on sequence similarity to assign a meaningful representative color. CRISPRStudio offers versatility to suit different biological contexts by including options such as automatic sorting of CRISPR loci and highlighting of shared spacers, while remaining fast and user-friendly. View Full-Text
Keywords: CRISPR; typing; software; visualization; viral origin; phage CRISPR; typing; software; visualization; viral origin; phage
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Dion, M.B.; Labrie, S.J.; Shah, S.A.; Moineau, S. CRISPRStudio: A User-Friendly Software for Rapid CRISPR Array Visualization. Viruses 2018, 10, 602.

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