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

被引:35
|
作者
Dion, Moira B. [1 ,2 ]
Labrie, Simon J. [3 ]
Shah, Shiraz A. [4 ]
Moineau, Sylvain [1 ,2 ]
机构
[1] Univ Laval, Fac Sci & Genie, Dept Biochim Microbiol & Bioinformat, Quebec City, PQ G1V 0A6, Canada
[2] Univ Laval, Fac Med Dent, Grp Rech Ecol Buccale, Quebec City, PQ G1V 0A6, Canada
[3] SyntBioLab Inc, 4820 Rue Pascaline, Levis, PQ G6W OL9, Canada
[4] Univ Copenhagen, COPSAC, Copenhagen Prospect Studies Asthma Childhood, Herlev & Gentofte Hosp, Ledreborg Alle 34, DK-2820 Gentofte, Denmark
来源
VIRUSES-BASEL | 2018年 / 10卷 / 11期
基金
加拿大自然科学与工程研究理事会; 加拿大健康研究院;
关键词
CRISPR; typing; software; visualization; viral origin; phage; MOLECULAR CHARACTERIZATION; ESCHERICHIA-COLI; EVOLUTION; RESISTANCE; SEQUENCE; COMBINATION; DIVERSITY; LOCI;
D O I
10.3390/v10110602
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
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.
引用
收藏
页数:11
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