Document Type

Article

Publication Date

8-1-2022

Publication Title

CRISPR J

Keywords

JGM, JCC, Algorithms, CRISPR-Cas Systems, Gene Editing, Genome, Software

JAX Source

CRISPR J. 2022;5(4):618-28.

Volume

5

Issue

4

First Page

618

Last Page

628

ISSN

2573-1602

PMID

35830604

DOI

https://doi.org/10.1089/crispr.2022.0042

Grant

This study was supported by the National Human Genome Research Institute Grant No. R01HG009900 (to A.W.C.), Arizona State University startup grant (to A.W.C.), and Jackson Laboratory internal grants (to A.W.C.).

Abstract

Zinc finger protein-, transcription activator like effector-, and CRISPR-based methods for genome and epigenome editing and imaging have provided powerful tools to investigate functions of genomes. Targeting sequence design is vital to the success of these experiments. Although existing design software mainly focus on designing target sequence for specific elements, we report here the implementation of Jackie and Albert's Comprehensive K-mer Instances Enumerator (JACKIE), a suite of software for enumerating all single- and multicopy sites in the genome that can be incorporated for genome-scale designs as well as loaded onto genome browsers alongside other tracks for convenient web-based graphic-user-interface-enabled design. We also implement fast algorithms to identify sequence neighborhoods or off-target counts of targeting sequences so that designs with low probability of off-target can be identified among millions of design sequences in reasonable time. We demonstrate the application of JACKIE-designed CRISPR site clusters for genome imaging.

Comments

This Open Access article is distributed under the terms of the Creative Commons License [CC-BY]

(http:// creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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