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1. Introduction to sgRNAble

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Noonanav edited this page Nov 16, 2021 · 7 revisions

sgRNAble is a tool for high-throughput design of sgRNA libraries targeting selected genes or whole genomes, while considering both on-target binding potential and off-target effects of a given sgRNA in a user-defined genome.

About sgRNAble

With increasing interest in the genetic engineering of non-model organism, there is a need for computational tools to assist in the transfer of biotechnologies between host systems. sgRNAble considers both on-target and off-target binding in the design of CRISPR-Cas9 single guide RNAs (sgRNAs) targeting genes in a user-defined host genome. Most sgRNA design tools are either specific to predefined host genomes or do not consider the off-target effects of a specific sgRNA sequence.

sgRNAble provides a tool for sgRNA design in novel host genomes by integrating:

  1. A framework for the defining of a host genome, including sequence and copy number of chromosomal and / or plasmid DNA
  2. A machine learning based on-target binding potential prediction tool1
  3. A biophysical model of Cas9 binding mechanics that considers genome-independent thermodynamics and kinetics of Cas9-sgRNA complexing, genome walking, site selection, R-loop formation and Cas9 cleavage2 (Figure 1)

Figure 1: This figure shows the various processes represented in the biophysical model of Cas9 binding mechanics imployed by sgRNAble. (Farasat, I., & Salis, H. M. (2016))

The combination of these tools enables sgRNAble to select optimal sgRNA sequences that simultaneously maximize on-target binding, while minimizing the likelihood of off-target binding throughout a user-defined host genome.

Citation

If you find sgRNAble useful in your research, please cite the following papers [TO BE UPDATED]:

  1. Doench, J. G., et al. (2016). Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nature biotechnology, 34, 184. doi:10.1038/nbt.3437

  2. Farasat, I., & Salis, H. M. (2016). A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation. PLOS Computational Biology, 12(1), e1004724. doi:10.1371/journal.pcbi.1004724

Contact

For any inquiries or issues on source code, please contact Steven Hallam and Avery Noonan at: [email protected] and [email protected]

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