The Gene Sculpt Suite: a Set of Tools for Genome Editing

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2019 May 26

PMID 31127311

Citations 11

Authors

Carla M Mann

Gabriel Martinez-Galvez

Jordan M Welker

Wesley A Wierson

Hirotaka Ata

Maira P Almeida

Karl J Clark

Jeffrey J Essner

Maura McGrail

Stephen C Ekker

Drena Dobbs

Affiliations

Soon will be listed here.

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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GeneWeld: Efficient Targeted Integration Directed by Short Homology in Zebrafish.

Welker J, Wierson W, Almeida M, Mann C, Torrie M, Ming Z Bio Protoc. 2021; 11(14):e4100.

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