Abstract
The discovery and development of DNA-editing nucleases (Zinc Finger Nucleases, TALENs, CRISPR/Cas systems) has given scientists the ability to precisely engineer or edit genomes as never before. Several different platforms, protocols and vectors for precision genome editing are now available, leading to the development of supporting web-based software. Here we present the Gene Sculpt Suite (GSS), which comprises three tools: (i) GTagHD, which automatically designs and generates oligonucleotides for use with the GeneWeld knock-in protocol; (ii) MEDJED, a machine learning method, which predicts the extent to which a double-stranded DNA break site will utilize the microhomology-mediated repair pathway; and (iii) MENTHU, a tool for identifying genomic locations likely to give rise to a single predominant microhomology-mediated end joining allele (PreMA) repair outcome. All tools in the GSS are freely available for download under the GPL v3.0 license and can be run locally on Windows, Mac and Linux systems capable of running R and/or Docker. The GSS is also freely available online at www.genesculpt.org.
Highlights
Recent additions to the gene editing toolbox include methods for identification of off-target sites [1,2], strategies for improving nuclease specificity [3] and the expansion of nuclease targeting capabilities [4,5,6,7]
Other approaches have focused on DNA double-strand break (DSB) repair by increasing the efficiency of homology-directed repair (HDR)/homologous recombination (HR) or enhancing the precision of the non-homologous end joining (NHEJ) DNA repair pathway [8]
Each tool was built in R using RStudio and is an RShiny application contained in a Docker image using the Open Analytics r-base image
Summary
Recent additions to the gene editing toolbox include methods for identification of off-target sites [1,2], strategies for improving nuclease specificity [3] and the expansion of nuclease targeting capabilities [4,5,6,7]. W176 Nucleic Acids Research, 2019, Vol 47, Web Server issue catch-all term for repair methods such as MMEJ and SSA, which utilize short regions of sequence homology to repair DSBs. GTagHD aids researchers in implementing the GeneWeld protocol, which leverages HMEJ repair to introduce targeted knock-ins with efficiencies much higher than previously reported [15].
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