Enhanced guide-RNA design and targeting analysis for precise CRISPR genome editing of single and consortia of industrially relevant and non-model organisms

Abstract Motivation Genetic diversity of non-model organisms offers a repertoire of unique phenotypic features for exploration and cultivation for synthetic biology and metabolic engineering applications. To realize this enormous potential, it is critical to have an efficient genome editing tool for...

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Bibliographic Details
Published in:Bioinformatics 2018-01, Vol.34 (1), p.16-23
Main Authors: Mendoza, Brian J, Trinh, Cong T
Format: Article
Language:English
Subjects:
Bacteria - genetics
CRISPR-Cas Systems
Eukaryota - genetics
Gene Editing - methods
Genomics - methods
RNA, Guide, CRISPR-Cas Systems
Software
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Summary:Abstract Motivation Genetic diversity of non-model organisms offers a repertoire of unique phenotypic features for exploration and cultivation for synthetic biology and metabolic engineering applications. To realize this enormous potential, it is critical to have an efficient genome editing tool for rapid strain engineering of these organisms to perform novel programmed functions. Results To accommodate the use of CRISPR/Cas systems for genome editing across organisms, we have developed a novel method, named CRISPR Associated Software for Pathway Engineering and Research (CASPER), for identifying on- and off-targets with enhanced predictability coupled with an analysis of non-unique (repeated) targets to assist in editing any organism with various endonucleases. Utilizing CASPER, we demonstrated a modest 2.4% and significant 30.2% improvement (F-test, P 
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btx564