# Open Vector Editor

## Specs

| Label                     | Value                         |
| ------------------------- | ----------------------------- |
| **Version**               | 3.0.0 (updated on 2025-05-28) |
| **Developer**             | Labii Inc.                    |
| **Type**                  | Section                       |
| **Support Configuration** | No                            |

## Overview

The Open Vector Editor widget integrates TeselaGen's Open Vector Editor (OVE) directly into Labii so users can view, design, edit, and annotate plasmids and DNA sequences inside ELN and LIMS records. It supports circular and linear sequence views, feature annotations, cut-site inspection, virtual digests, and alignment workflows in one interactive editing environment. This widget is well suited for molecular cloning, plasmid verification, synthetic biology, and sequence documentation tasks where scientists need both a graphical map and sequence-level editing tools. By keeping sequence design and analysis in the same record as the rest of the experiment data, the widget improves traceability and collaboration.

## Use Cases

* **Plasmid Design**: Build new plasmid constructs by entering DNA sequences and annotating promoters, coding regions, tags, and markers.
* **Sequence Verification**: Review imported plasmid files, inspect cut sites, and validate annotated features before downstream experiments.
* **Cloning Workflows**: Simulate restriction digests and manage sequence edits during cloning and assembly planning.
* **Inventory Documentation**: Store plasmid sequences and annotations alongside inventory, storage, and usage records in Labii.
* **Annotation Automation**: Apply feature libraries or primer libraries to sequences to accelerate repetitive annotation tasks.

## Interface

### Read-only View

In read-only mode, the widget presents the saved sequence record without exposing the editing toolbar. Users can review the plasmid or sequence map, sequence annotations, and other saved analysis outputs as part of the record. This view is useful for record review, handoff, and audit-friendly inspection because it keeps the documented sequence visible while preventing accidental modification.

* **Data Display**: Displays the saved sequence map and associated annotations.
* **Navigation**: Lets users inspect the visual representation of the current construct in the record.
* **Export Options**: Export actions are not available until the widget is opened in edit mode.
* **Search/Filter**: Search and editing tools are hidden in read-only mode.

<figure><img src="/files/JttRoTimfk7HlMESucqt" alt="Read-only view of the Open Vector Editor widget"><figcaption><p>The read-only view displays the saved sequence record and annotations without the editing controls.</p></figcaption></figure>

### Edit View

In edit mode, the full OVE workspace opens so users can import sequences, switch between circular and linear views, annotate sequence features, inspect cut sites, and run supporting analysis tools. The main workspace combines a graphical map, a sequence viewer, and supporting panels for properties, features, and analysis outputs. This layout lets users move between visual construct editing and base-level sequence operations without leaving the record.

* **Input Methods**: Paste raw sequence text or import supported sequence files such as GenBank, ApE, FASTA, AB1, SnapGene, and related formats.
* **Formatting Options**: Switch among circular, linear, and other supported sequence views while displaying annotations and digest information.
* **Validation**: Inspect annotations, alignment outputs, and cut sites before saving changes back to the record.
* **Collaboration**: Save updated sequence records into Labii so other team members can review the latest construct state.

## Configuration

The Open Vector Editor widget does not require widget-level configuration before use. Once the widget is added to a section, users can immediately load or enter sequence data and begin editing.

{% hint style="info" %}
Because the widget has no separate settings panel, behavior is driven by the sequence data loaded into the editor and the analysis tools the user chooses during editing.
{% endhint %}

## Additional Functions

### Import Sequence

Open Vector Editor supports importing sequence data from common molecular biology file formats, including `.gb`, `.gbk`, `.ape`, `.ab1`, `.fasta`, `.fas`, `.json`, `.xml`, `.seq`, `.sbd`, and `.dna`.

{% stepper %}
{% step %}
Open the record and click **Edit** on the Open Vector Editor section.
{% endstep %}

{% step %}
Click **Open** in the toolbar, or drag a supported file onto the cloud icon.
{% endstep %}

{% step %}
Select the sequence file to import.
{% endstep %}

{% step %}
Review the loaded construct in the editor and save the record when finished.
{% endstep %}
{% endstepper %}

### Export Sequence

Sequences can be exported for sharing or downstream analysis in formats such as GenBank, FASTA, and TeselaGen JSON.

{% stepper %}
{% step %}
Open the widget in edit mode.
{% endstep %}

{% step %}
Use **File** and select the export action for sequences.
{% endstep %}

{% step %}
Choose the desired export format and download the file.
{% endstep %}
{% endstepper %}

### Change Sequence and Features

The widget supports direct sequence editing together with feature creation, editing, and deletion.

{% stepper %}
{% step %}
Load or paste a sequence into the editor.
{% endstep %}

{% step %}
Select a sequence region in the editor.
{% endstep %}

{% step %}
Use the toolbar to insert bases, edit selected bases, delete selected bases, copy sequence, or create and update a feature.
{% endstep %}

{% step %}
Review the updated map and sequence view, then save the record.
{% endstep %}
{% endstepper %}

### Restriction Digest and Cut Sites

OVE includes enzyme and cut-site tools for planning cloning workflows and evaluating sequence manipulation strategies.

{% stepper %}
{% step %}
Open the sequence in edit mode.
{% endstep %}

{% step %}
Add enzymes or open the relevant digest or cut-site view in the workspace.
{% endstep %}

{% step %}
Review recognition sites, cut positions, and fragment information for the current construct.
{% endstep %}
{% endstepper %}

### Auto Annotate

Labii supports automated annotation in OVE using CSV feature libraries or ApE feature files so users can quickly label commonly used sequence elements.

{% embed url="<https://youtu.be/EvVG9LpBiak>" %}

<figure><img src="/files/njqavEulVsWBVCvAaZA2" alt="Open Vector Editor auto-annotation workflow"><figcaption><p>The auto-annotation workflow matches sequence regions against uploaded feature libraries and applies annotations automatically.</p></figcaption></figure>

{% stepper %}
{% step %}
In the editor toolbar, open **Tools** and select **Auto Annotate**.
{% endstep %}

{% step %}
Choose whether to auto annotate features, parts, or primers.
{% endstep %}

{% step %}
Upload or select a CSV or ApE feature file.
{% endstep %}

{% step %}
Review the generated annotations and adjust them manually if needed.
{% endstep %}
{% endstepper %}

### Sequence Alignment

The alignment tool compares the active sequence against an input sequence so users can review sequence similarity and confirm construct identity.

{% embed url="<https://youtu.be/Syoei-6n198>" %}

<figure><img src="/files/Jw5uGAdEgoWxiwp502Kp" alt="Open Vector Editor sequence alignment panel"><figcaption><p>The alignment panel shows the comparison between the current construct and an input sequence for verification and review.</p></figcaption></figure>

{% stepper %}
{% step %}
Open the widget in edit mode and click the **Alignment** icon in the toolbar.
{% endstep %}

{% step %}
Provide an alignment name, sequence name, the sequence to compare, and whether reverse-complementing is needed.
{% endstep %}

{% step %}
Click **Submit** to generate the alignment.
{% endstep %}

{% step %}
Review the alignment panel and save the record to keep the result.
{% endstep %}
{% endstepper %}

### Fullscreen and Standalone Review

Users can enlarge the editor interface to focus on sequence review and editing without distraction from other record sections.

{% stepper %}
{% step %}
Open the widget in edit mode.
{% endstep %}

{% step %}
Use **Fullscreen** or **Standalone** from the available interface actions.
{% endstep %}

{% step %}
Review or edit the construct in the expanded workspace, then save changes back to the record.
{% endstep %}
{% endstepper %}

## Best Practices

### Sequence Management

* Import authoritative sequence files, such as curated GenBank or SnapGene exports, whenever possible instead of relying on manually retyped sequences.
* Use clear construct names and feature labels so downstream users can understand the plasmid record without reopening raw source files.
* Save sequence changes after each major editing step to keep the record synchronized with the current design.

### Annotation Quality

* Review auto-generated annotations before accepting them as final, especially for overlapping features or ambiguous matches.
* Standardize feature naming across projects so searches, comparisons, and exports remain consistent.
* Confirm strand direction, start and end positions, and feature type before finalizing a plasmid map.

### Workflow Reliability

* Check cut sites and virtual digest results before ordering primers, enzymes, or cloning reagents.
* Use the alignment tool to verify sequence identity when comparing expected and observed constructs.
* Prefer the same editor across related projects when consistency of visualization and annotation behavior matters.

{% hint style="success" %}
Using imported reference files, standardized annotations, and saved intermediate edits helps maintain reliable plasmid records and reduces rework during cloning and verification.
{% endhint %}

### Common Pitfalls to Avoid

* **Avoid** saving a construct without reviewing imported annotations, because imported files may contain outdated or inconsistent feature labels.
* **Avoid** making large sequence edits without rechecking cut sites and alignments afterward.
* **Instead** verify the edited construct with digest and alignment tools before treating the record as final.

## Related Widgets

* [**Plasmid Editor**](/widgets/section-widgets/biology/molecular-biology-suite/plasmid-editor.md): Use this widget when you need another plasmid-focused editing workflow with sequence map and feature management inside the same molecular biology suite.

## References

* [Open Vector Editor on GitHub](https://github.com/TeselaGen/tg-oss/tree/master/packages/ove) - Source project for the embedded OVE editor.
* [Molecular Biology Suite](/widgets/section-widgets/biology/molecular-biology-suite.md) - Category overview for related sequence analysis widgets in Labii.
* [ApE Feature Files](https://jorgensen.biology.utah.edu/wayned/ape/) - Reference format supported by the auto-annotation workflow.


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