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 journalArticle

1 Citation (Scopus)

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 languageEnglish (US)
Pages (from-to)W175-W182
JournalNucleic acids research
Volume47
Issue numberW1
DOIs
StatePublished - Jul 2 2019

Fingerprint

CRISPR-Cas Systems
DNA End-Joining Repair
Genes
Double-Stranded DNA Breaks
Deoxyribonucleases
Zinc Fingers
Licensure
Oligonucleotides
Software
Alleles
Genome
Gene Editing
Transcription Activator-Like Effector Nucleases
Machine Learning

ASJC Scopus subject areas

  • Genetics

Cite this

Mann, C. M., Martínez-Gálvez, G., Welker, J. M., Wierson, W. A., Ata, H., Almeida, M. P., ... Dobbs, D. (2019). The Gene Sculpt Suite: a set of tools for genome editing. Nucleic acids research, 47(W1), W175-W182. https://doi.org/10.1093/nar/gkz405

The Gene Sculpt Suite : a set of tools for genome editing. / Mann, Carla M.; Martínez-Gálvez, Gabriel; Welker, Jordan M.; Wierson, Wesley A.; Ata, Hirotaka; Almeida, Maira P.; Clark, Karl J; Essner, Jeffrey J.; McGrail, Maura; Ekker, Stephen C; Dobbs, Drena.

In: Nucleic acids research, Vol. 47, No. W1, 02.07.2019, p. W175-W182.

Research output: Contribution to journalArticle

Mann, CM, Martínez-Gálvez, G, Welker, JM, Wierson, WA, Ata, H, Almeida, MP, Clark, KJ, Essner, JJ, McGrail, M, Ekker, SC & Dobbs, D 2019, 'The Gene Sculpt Suite: a set of tools for genome editing', Nucleic acids research, vol. 47, no. W1, pp. W175-W182. https://doi.org/10.1093/nar/gkz405
Mann CM, Martínez-Gálvez G, Welker JM, Wierson WA, Ata H, Almeida MP et al. The Gene Sculpt Suite: a set of tools for genome editing. Nucleic acids research. 2019 Jul 2;47(W1):W175-W182. https://doi.org/10.1093/nar/gkz405
Mann, Carla M. ; Martínez-Gálvez, Gabriel ; Welker, Jordan M. ; Wierson, Wesley A. ; Ata, Hirotaka ; Almeida, Maira P. ; Clark, Karl J ; Essner, Jeffrey J. ; McGrail, Maura ; Ekker, Stephen C ; Dobbs, Drena. / The Gene Sculpt Suite : a set of tools for genome editing. In: Nucleic acids research. 2019 ; Vol. 47, No. W1. pp. W175-W182.
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