Plasmid Editor Help

Open a sequence

Choose a GenBank, ApE, EMBL, SnapGene .dna, FASTA, plain DNA or saved project file. You can also drop a file onto the upload area. Use “Paste a sequence instead” for DNA, FASTA, GenBank or EMBL text. If the file contains several records, use the Record selector to switch between them.

The vector’s name appears above the map and inside it. SnapGene files use their enabled custom map label when present. A generic GenBank LOCUS name such as “Exported” falls back to the filename, or a short definition when the filename is also generic. Use Record settings or the map’s “Rename vector” menu action to change the name.

Sequence files can be up to 25 MiB, projects up to 80 MiB, and individual records up to 5 million bases. FASTA and plain DNA contain no feature table, so they start without annotations. The editor displays supplied annotations; it does not identify missing features automatically.

GenBank, ApE and EMBL support ranges, reverse strands, joined segments and uncertain endpoints. Remote or unsupported locations are retained as text but cannot be fully mapped. Resolve these locations before editing the sequence. Review Import details for warnings specific to your file.

SnapGene import reads the DNA, topology and annotated features. Original packets, including primers, notes and history, are retained in the saved project. Primer objects, alignments and SnapGene history are not editable.

Edit annotations

A feature is an annotation attached to a base range: it has a name, type and optional notes. Right-click a feature arrow, label or table row to copy its DNA, rename it, edit its notes, or choose either deletion action. Copying a feature includes all its joined segments in biological orientation. Rename changes its label and supports Undo/Redo without changing its coordinates or DNA. “Delete annotation” removes the feature while keeping the DNA. “Delete annotated DNA” removes its exact base segments and reviews the effect on other annotations before confirmation. For a joined feature, DNA between the listed segments is kept.

To annotate a new region, select bases and right-click the selection, then choose “Add feature / note”. Enter a name and any notes in the feature form, and save it. These annotations are retained in projects and supported annotated exports. The ordinary buttons also provide copying, renaming, note editing, annotation creation and annotation-only deletion. Use the context menu to delete the exact DNA segments of an annotation. Keyboard users can open the menu with Shift+F10 or the Menu key.

Select a feature in the map or table to edit its name, type, location and notes. Use “Add feature” to create an annotation. Locations are 1-based and inclusive: 10..100 describes a range, complement(10..100) places it on the reverse strand, and join(…) combines segments.

Open Annotation fields to edit qualifiers such as gene, product and note. Repeated fields retain their order; “Flag only” creates a field without a value. The name and note controls update their first matching qualifier. Advanced JSON editing is also available. Choose “Save feature” to apply the changes.

Colours and map symbols

Choose from the 40 colour boxes, or open More colour options for a custom picker and optional hex value. Imported colours, including differently coloured segments, remain until you change them. A new colour replaces the feature’s segment colours. “Restore imported colours” uses the retained source appearance where the segments still match.

The map offers arrows, blocks, bent promoter arrows and T-shaped terminator marks, with automatic or feature-type defaults. Forward and reverse change the annotation strand without changing the DNA; this can invalidate an existing CDS translation. Bidirectional and nondirectional change the arrows while retaining the biological strand. Symbols indicate the annotated region rather than a precise transcription start or stop site.

For several features, use the table checkboxes and open Edit multiple features. Select all matching includes matches beyond the visible table rows; selection by type applies to the whole record. The operation includes selected features hidden by a later search. Unchosen appearance properties, locations, strands and other annotations remain unchanged. Undo reverses the entire batch.

Inspect the map and sequence

Circular and Linear switch the map view without changing the record’s actual topology. Zoom, rotation and Reset view change the display. Use Record settings to change the topology or base-1 position. On narrow screens, scroll sideways within the map to see its full width.

The map draws up to 1,000 matching features. It normally labels 20 features, or 10 features and 10 cuts when restriction sites are shown; selecting an item can add a label. Search by feature name, type or note to narrow dense records. The table and sequence view load bounded batches for responsiveness.

Choose Show sequence to inspect bases. Click a base and Shift-click another to extend a selection, or select a range by coordinates. On a circular record, an end coordinate before the start selects across the origin.

Restriction sites

Enable Restriction sites to scan the current record locally with the built-in enzyme catalogue. Filter by enzyme name or choose unique cutters. Unique means one detected, fully cleavable site. Map ticks mark top-strand cut boundaries; circular position 0 marks the origin. Select a cut for details of both strands.

These are sequence-based predictions. Methylation, star activity and reaction conditions are not modelled. Counts and any displayed limits are shown with the results.

Find and copy DNA

Search for a DNA or IUPAC pattern of up to 1,000 bases. Both strands are searched, including across a circular origin. An ambiguous reference base matches only when all of its possible bases fit the pattern. The total match count is retained, with navigation through up to 1,000 matches.

Copy selected bases, a selected feature or the whole sequence. Feature copying joins its segments in biological 5′ to 3′ orientation. Copy reverse complement reverses and complements the chosen DNA. If clipboard access is unavailable, a dialog lets you select and copy the text manually.

Edit DNA and undo changes

Choose Edit sequence to replace, insert or delete bases. Review edit shows the insertion position or exact inclusive range, the number of bases being added or removed, and the resulting sequence length before anything changes. It lists annotations that will disappear separately from those that will be altered. Cancel keeps the original record; the confirmation button applies the edit. Manual sequence edits use a contiguous interval in the current coordinate system. For an edit crossing a circular origin, choose a suitable new origin first or make two edits.

Coordinates shift with the edit. Features intersecting changed bases are flagged for review, and invalid translations are removed from active qualifiers. Deleted features are recorded in project history. Undo and Redo restore applied changes to the sequence and annotations together.

Record name, topology and origin

Record settings changes the name, actual topology or circular base-1 position in one Undo step. Save a topology change before choosing a new circular origin. Unlike rotating the map, changing the origin rotates the DNA and remaps annotations.

An origin change requires exact, local feature locations without ordered segments. Supported transl_except, anticodon and simple rpt_unit_range coordinates are remapped. Choose an origin outside a repeat unit so its range stays contiguous. Unsupported changes are refused before anything is applied. Coordinates in free-text notes and the original import snapshot remain unchanged.

Save and export

Save project retains the records, annotations, display settings, original import metadata and edit-history metadata for reopening. A project does not restore the in-memory Undo stack. Export writes the current record in the selected format:

GenBank

Annotated sequence exchange, including supported locations and qualifiers. Optional colour and symbol hints may be ignored by other applications.

SnapGene .dna

Current DNA, name, topology, exact local feature locations, strands, colours and qualifiers. Uncertain, remote, between-base, ordered or mixed-strand locations are refused; use GenBank or a project for those records. Original primer objects, history, alignments and opaque packets stay in the project and are not copied into the new .dna file. Other applications may ignore custom symbol hints. Independent parser checks have passed, but opening these exports in SnapGene desktop remains unverified.

FASTA

Sequence only; annotations and display settings are omitted.

SVG

A sharp, scalable vector figure with the current appearance, exported at a default width of 1,600 pixels. Save a project as well if you want to continue editing the DNA.

Local recovery and privacy

Sequence processing runs in your browser without uploading the sequence. Local recovery is optional and starts off. Enabling it stores a separate workspace copy for each editing session, after a short delay following applied changes. Up to ten copies can be kept, with an 80 MiB limit per workspace. If saving fails, download a project; the previous successful copy is retained.

Recovery stores applied edits and workspace settings. Unsaved form entries and the in-memory Undo stack are not restored. Turning recovery off deletes all editor recovery copies in this browser. Browser cleanup, private browsing or storage restrictions can make a copy unavailable, so use downloaded projects for lasting backups.

Use the edited sequence with other tools

Export FASTA or copy the required DNA, then open Primer Designer, Restriction Site Analyzer or Primer Binding Checker and supply it there. Confirm the receiving tool's topology and coordinate range after an edit or origin change. Copying a reverse-strand feature produces its biological 5′ to 3′ sequence.

The editor does not design primers or provide direct send buttons. Other tools may accept sequence text while omitting annotations, and they have their own input limits. Checker and Primer Scan accept ten primer pairs per checking batch; supply the appropriate reference and run the calculation in the receiving tool.

Use maps in figures and presentations

Choose SVG in Export to save a vector map. It can be resized without raster pixelation and retains the current colours, feature symbols and displayed labels. Dense maps still use the display's feature and label limits; select important annotations or adjust the view before exporting. Check the saved figure at the size you intend to use.

Desktop PowerPoint supports inserting and resizing SVG images. Font substitution and label editing depend on the receiving application. Check your journal's accepted formats and final figure requirements; SVG export alone does not establish compliance with them.