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 via in silico 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/.
Highlights
DNA visualization software must 1) annotate features and depict DNA features graphically, 2) simulate molecular cloning techniques and 3) generate visually appealing output for figures.Good DNA visualization software applies meaning to a string of DNA bases
A biologist must be able to identify subsequences such as restriction enzyme recognition sequences, recombinase recognition sequences, and overlapping end sequences that are useful for particular recombinant techniques
Good DNA software provides powerful in silico simulation of common DNA manipulations, such as restriction digests or Gibson cloning
Summary
DNA visualization software must 1) annotate features and depict DNA features graphically, 2) simulate molecular cloning techniques and 3) generate visually appealing output for figures.Good DNA visualization software applies meaning to a string of DNA bases. Sequence-wide information is stored as a special COMMENT line that begins with the text “ApEinfo:” Second, each feature has additional feature-specific formatting data stored in feature qualifiers that begin with “/ApEinfo_.” Some GenBank parsers require qualifiers to be part of a controlled vocabulary, so ApE has a user-specified option in the preferences window to save files without this information. ApE uses this modular framework for the restriction enzyme set, the feature library, gel ladders, graphical arrowheads and user preferences.
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