GuideMaker: Software to design CRISPR-Cas guide RNA pools in non-model genomes. (1st April 2022)

• Record Type: Journal Article
• Authors: Poudel, Ravin; Rodriguez, Lidimarie Trujillo; Reisch, Christopher R; Rivers, Adam R
• Is Part Of: GigaScience. Volume 11(2022)
• Publication Date: 2022-04-01
• Subjects: PAM -- CRISPR-Cas -- gRNA -- Perturb-seq -- Hierarchical Navigable Small World graph; Information storage and retrieval systems -- Research -- Periodicals; Biology -- Research -- Periodicals; Medical sciences -- Research -- Periodicals; Database management -- Periodicals; 570.285
• DOI: 10.1093/gigascience/giac007
• Languages: English
• ISSNs: 2047-217X

Abstract

Abstract: Background: CRISPR-Cas systems have expanded the possibilities for gene editing in bacteria and eukaryotes. There are many excellent tools for designing CRISPR-Cas guide RNAs (gRNAs) for model organisms with standard Cas enzymes. GuideMaker is intended as a fast and easy-to-use design tool for challenging projects with (i) non-standard Cas enzymes, (ii) non-model organisms, or (iii) projects that need to design a panel of gRNA for genome-wide screens. Findings: GuideMaker can rapidly design gRNAs for gene targets across the genome using a degenerate protospacer-adjacent motif (PAM) and a genome. The tool applies hierarchical navigable small world graphs to speed up the comparison of guide RNAs and optionally provides on-target and off-target scoring. This allows the user to design effective gRNAs targeting all genes in a typical bacterial genome in ∼1–2 minutes. Conclusions: GuideMaker enables the rapid design of genome-wide gRNA for any CRISPR-Cas enzyme in non-model organisms. While GuideMaker is designed with prokaryotic genomes in mind, it can efficiently process eukaryotic genomes as well. GuideMaker is available as command-line software, a stand-alone web application, and a tool in the CyCverse Discovery Environment. All versions are available under a Creative Commons CC0 1.0 Universal Public Domain Dedication.