The Gene Sculpt Suite: a set of tools for genome editing 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
dc.contributor.department Genetics, Development and Cell Biology
dc.contributor.department Bioinformatics and Computational Biology 2020-04-07T17:46:09.000 2020-06-30T04:02:12Z 2020-06-30T04:02:12Z Tue Jan 01 00:00:00 UTC 2019 2019-07-02
dc.description.abstract <p>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 <em>Gene Sculpt Suite</em> (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 <a href="" target="_blank"></a>.</p>
dc.description.comments <p>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." <em>Nucleic acids research</em> 47, no. W1 (2019): W175-W182. doi: <a href="">10.1093/nar/gkz405</a>.</p>
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dc.identifier archive/
dc.identifier.articleid 1245
dc.identifier.contextkey 17238694
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath gdcb_las_pubs/241
dc.language.iso en
dc.source.bitstream archive/|||Fri Jan 14 22:52:47 UTC 2022
dc.source.uri 10.1093/nar/gkz405
dc.subject.disciplines Bioinformatics
dc.subject.disciplines Cell and Developmental Biology
dc.subject.disciplines Computational Biology
dc.subject.disciplines Genetics and Genomics
dc.title The Gene Sculpt Suite: a set of tools for genome editing
dc.type article
dc.type.genre article
dspace.entity.type Publication
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