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ApE, A Plasmid Editor: A Freely Available DNA Manipulation and Visualization Program

Overview
Journal Front Bioinform
Specialty Biology
Date 2022 Oct 28
PMID 36304290
Authors
M Wayne Davis
Erik M Jorgensen
Affiliations
Soon will be listed here.
Abstract

A plasmid Editor (ApE) is a free, multi-platform application for visualizing, designing, and presenting biologically relevant DNA sequences. ApE provides a flexible framework for annotating a sequence manually or using a user-defined library of features. ApE can be used in designing plasmids and other constructs simulation of cloning methods such as PCR, Gibson assembly, restriction-ligation assembly and Golden Gate assembly. In addition, ApE provides a platform for creating visually appealing linear and circular plasmid maps. It is available for Mac, PC, and Linux-based platforms and can be downloaded at https://jorgensen.biology.utah.edu/wayned/ape/.

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References
1.
Mansouri M, Bellon-Echeverria I, Rizk A, Ehsaei Z, Cosentino C, Silva C . Highly efficient baculovirus-mediated multigene delivery in primary cells. Nat Commun. 2016; 7:11529. PMC: 4857464. DOI: 10.1038/ncomms11529. View
2.
Pryor J, Potapov V, Kucera R, Bilotti K, Cantor E, Lohman G . Enabling one-pot Golden Gate assemblies of unprecedented complexity using data-optimized assembly design. PLoS One. 2020; 15(9):e0238592. PMC: 7467295. DOI: 10.1371/journal.pone.0238592. View
3.
Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth B, Remm M . Primer3--new capabilities and interfaces. Nucleic Acids Res. 2012; 40(15):e115. PMC: 3424584. DOI: 10.1093/nar/gks596. View
4.
Doench J, Hartenian E, Graham D, Tothova Z, Hegde M, Smith I . Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nat Biotechnol. 2014; 32(12):1262-7. PMC: 4262738. DOI: 10.1038/nbt.3026. View
5.
Li M, Elledge S . Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nat Methods. 2007; 4(3):251-6. DOI: 10.1038/nmeth1010. View