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

Carla M. Mann; Gabriel Martínez-Gálvez; Jordan M. Welker; Wesley A. Wierson; Hirotaka Ata; Maira P. Almeida; Karl J. Clark; Jeffrey J. Essner; Maura McGrail; Stephen C. Ekker; Drena Dobbs

doi:10.1093/nar/gkz405

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

Carla M. Mann, Gabriel Martínez-Gálvez, Jordan M. Welker, Wesley A. Wierson, Hirotaka Ata, Maira P. Almeida, Karl J. Clark, Jeffrey J. Essner, Maura McGrail, Stephen C. Ekker, Drena Dobbs

Research output: Contribution to journal › Article › peer-review

11 Scopus citations

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.

Original language	English (US)
Pages (from-to)	W175-W182
Journal	Nucleic acids research
Volume	47
Issue number	W1
DOIs	https://doi.org/10.1093/nar/gkz405
State	Published - Jul 2 2019
Externally published	Yes

Bibliographical note

Funding Information:
National Institutes of Health [R24 OD020166 to J.J.E., M.M., S.C.E., K.J.C., D.D., GM63904 to S.C.E., K.J.C.]. Funding for open access charge: National Institutes of Health [R24 OD020166].

Publisher Copyright:
© 2019 The Author(s).

PubMed: MeSH publication types

Journal Article
Research Support, N.I.H., Extramural

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

Abstract

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