ApE (A Plasmid Editor)

ApE (A Plasmid Editor) is a desktop sequence editor geared for molecular biologists who need a practical, no‑frills tool for everyday cloning and sequence analysis. It runs on Windows and macOS (with Linux builds available) and is distributed as freely usable software with optional donations to support development. ApE focuses on editable sequence windows, linked graphic/text maps and a broad toolset that covers restriction mapping, primer discovery, basic sequence alignment and popular assembly workflows (Golden Gate and Gibson). Core capabilities center on interactive sequence visualization and manipulation. The editor highlights restriction sites (with correct Dam/Dcm methylation handling), shows translations, open reading frames, %GC and melting temperature in real time for any selection, and can annotate features using pre‑defined or custom feature libraries. Graphic maps (linear or circular) are generated from annotated files and can be saved as EPS or SVG (and Windows metafile copy on Windows) for publication or posters. ApE reads and writes common lab formats — FASTA, GenBank, EMBL and DNA Strider formats — and has extended support for ABI trace files, FASTQ (with Phred visibility), SBOL v1 import and GFF3 tracks, enabling easy exchange with sequence repositories and other tools. Practical lab tools are built into the UI. The primer-finding dialog searches for primers matching user constraints (length, Tm, %GC, self/other complementarity), and primers can be highlighted and linked on maps. The PCR dialog and a Quick‑PCR function support routine amplicon planning. Molecular calculators and recipe helpers (including QR export) assist in setting up equimolar reactions. For cloning workflows, ApE includes Golden Gate and Gibson wizards that calculate reaction parameters and can assemble designs while adding feature annotations; diagnostic digest windows help pick enzyme sets and detect SNIP/SNPs by selecting sites that differ between sequences. Users may define enzyme sets and groups (for “in-stock” or Golden Gate enzyme groups) and import enzyme definitions from REBASE-style files. Sequence QC and trace work are well supported: ABI trace files can be opened and aligned directly to a reference, with alignments hyperlinked back to the trace view. The X-ray/ABI window shows traces and allows basecall inspection; FASTQ files open as locked sequences with Phred values visible and searchable. ApE can export genomic regions and integrate feature tracks from WormBase (via GFF3/FASTA export) and provides a direct BLAST link to NCBI or WormBase for selected sequences. Feature scanning can add primer sequences into qualifiers and supports amino‑acid feature definitions, letting users quickly annotate motifs and protein features. ApE also contains many convenience and customization options: create and edit custom enzymes and feature libraries, configure map label boxes and themes (including a dark mode), export publication-quality graphics, and copy links between text and graphics by double-clicking. The tool has active maintenance and bugfix history, and supports workflows like finding translationally silent restriction sites, aligning sequences to ABI traces, generating DNA ladders for gel planning, and printing sequence windows. This combination of accessible UI, focused cloning/annotation tools and broad file-format interoperability makes ApE an effective companion for bench scientists who want local, dependable sequence editing without subscription overhead.