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 journalArticlepeer-review

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

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]. Conflict of interest statement. Iowa State University and The Mayo Clinic have filed for patent protection for the Ge-neWeld targeted knock-in technology. W.W., J.E., M.M., K.C. and S.C.E. have financial interests and/or management roles in LIFEngine Technologies Inc., a licensee of the GeneWeld technology.

PubMed: MeSH publication types

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

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