The Gene Sculpt Suite: a set of tools for genome editing

Date
2019-07-02
Authors
McGrail, Maura
Mann, Carla
Martínez-Gálvez, Gabriel
Essner, Jeffrey
Welker, Jordan
Wierson, Wesley
Ata, Hirotaka
Almeida, Maira
Clark, Karl
Essner, Jeffrey
McGrail, Maura
Ekker, Stephen
Dobbs, Drena
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Genetics, Development and Cell BiologyBioinformatics and Computational Biology
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.

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This article is published as Mann, Carla M., Gabriel Martínez-Gálvez, Jordan M. Welker, Wesley A. Wierson, Hirotaka Ata, Maira P. Almeida, Karl J. Clark et al. "The Gene Sculpt Suite: a set of tools for genome editing." Nucleic acids research 47, no. W1 (2019): W175-W182. doi: 10.1093/nar/gkz405.

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