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Phage Genetic Engineering Using CRISPR–Cas Systems
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Viruses 2018, 10(11), 602;

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

Département de Biochimie, de Microbiologie, et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada
Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec City, QC G1V 0A6, Canada
SyntBioLab Inc., 4820 rue de la Pascaline, Lévis, QC G6W 0L9, Canada
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)
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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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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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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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