Open Vector Editor

OVE enables users to view, design, edit, and annotate plasmids and their DNA sequences with an intuitive graphical interface.

Overview

The Labii Open Vector Editor widget integrates the Open Vector Editor (OVE)—an open-source, user-friendly tool developed by TeselaGen—directly into the Labii platform. Available at https://github.com/TeselaGen/tg-oss/tree/master/packages/ove, OVE enables users to view, design, edit, and annotate plasmids and their DNA sequences with an intuitive graphical interface. This widget supports both circular and linear views, feature annotations, enzyme cut sites, and sequence manipulation, making it ideal for molecular biologists working with genetic constructs. By embedding OVE, Labii empowers researchers with a powerful visual and interactive sequence editor as part of its molecular biology suite.

Use case

• Plasmid Design and Annotation - Researchers can design new plasmids by entering DNA sequences and annotating key features like promoters, ORFs, selection markers, and tags.

• Inventory Management - Integrated with Labii’s data platform, the plasmid editor can help manage plasmid inventories by linking sequence data with sample storage and usage records.

Key Features

• Dual Sequence Views: OVE provides synchronized circular and linear representations of DNA sequences, allowing users to interactively select and edit features across both views. 

• Feature Annotation: Users can add, modify, and manage genetic features such as promoters, genes, restriction sites, and origins of replication. The editor supports both canonical and non-canonical features, with options to import features via CSV or GenBank files. 

• Auto-Annotation: OVE includes an auto-annotation feature that can automatically identify and annotate features within a DNA sequence, streamlining the annotation process. 

• Restriction Digest Simulation: The tool allows users to simulate restriction enzyme digestions, providing visual outputs of expected fragment sizes and enabling virtual gel electrophoresis analysis. 

• Primer Design and Management: OVE supports the design and management of primers, facilitating PCR simulations and other molecular biology workflows.

• Protein Translation: Users can translate DNA sequences into amino acid sequences, aiding in protein analysis and engineering. 

• File Format Support: OVE supports various file formats, including GenBank (.gb, .gbk), FASTA (.fasta), SnapGene (.dna), and SBOL (.xml), ensuring compatibility with other bioinformatics tools.

How to Use

Follow these steps to begin using the Open Vector Editor:

1. Add the Widget: Add a new section in your record and select the widget type Open Vector Editor.

2. Import or Paste Sequences:

   • Paste raw DNA sequence directly.

   • Or import from standard file formats like .gb, .gbk, .ape.

3. Explore the Interface:

   • Left Panel: Circular or linear map of the sequence.

   • Right Panel: Text-based display showing nucleotide sequence, translation, and annotated features.

4. Fullscreen Mode: Click Fullscreen to expand the editor and focus on your work.

5. Standalone View: Click Standalone to open the editor in a dedicated view that hides all other sections.

Import Sequence

OVE supports importing sequences from several file formats:

• Supported file types: .gb, .gbk, .ape, .ab1

• To import: File → Import Sequence

Export Sequence

Sequences can be exported for sharing or external analysis. Supported export formats include:

• GenBank File (.gb/.gbk)

• FASTA

• TeselaGen JSON

To export:

File → Export Sequences

Edit Sequence Features

Once the widget is added:

• Load a sequence by pasting or importing it.

• Features will auto-populate based on the sequence file.

To Modify Features:

• Highlight a region of the sequence.

• Right-click to Create, Edit, or Delete a feature.

To Manage Feature Details:

1. Click the Properties tab on the right panel.

2. Navigate to the Features tab.

3. Select or create a feature.

4. Use:

   • New: Create a new feature.

   • Edit: Modify selected feature’s name, type, strand, or color.

   • Delete: Remove the feature from the sequence.

Manage Restriction Sites

All restriction enzyme cut sites are listed under the Cutsites tab. Use this list to view enzyme recognition sites and plan your cloning strategy.

Virtual Digest

The Virtual Digest tool allows simulation of restriction enzyme digests:

• View fragment sizes produced by selected enzymes.

• Analyze results as you would with gel electrophoresis.

This feature is essential for planning in silico cloning workflows.

Auto Annotate

Auto annotation is a common bioinformatics technique used to automatically identify and label features within a biological sequence—such as genes, promoters, CDS regions, primers, parts, or other functional elements. Instead of manually scanning a long DNA or protein sequence, auto annotation compares the sequence against known feature libraries (e.g., CSV or ApE feature files) and then highlights all matching regions. This greatly accelerates molecular cloning workflows, genome annotation, plasmid verification, and primer design.

Labii provides a built-in Auto Annotate tool that allows users to annotate sequences instantly using their own reference feature lists. Whether you maintain a corporate plasmid library, standardized parts registry, or a set of commonly used primers, Labii can automatically map them onto any sequence.

Supported Source Files

Labii supports automatic annotation from either:

• CSV Files. A simple tabular file containing feature names, types, and sequences. This is ideal for organizations maintaining their own part registries.

• ApE Feature Files. ApE (A plasmid Editor) feature lists are popular in molecular biology. You can import existing ApE feature files without modification.

Labii reads these files and matches each element against your sequence to generate annotations.

How to Use Auto Annotate in Labii

You can run auto annotation on any DNA or protein sequence directly inside Labii’s sequence editor.

Steps:

1

In the sequence viewer/editor, click Tools in the toolbar.

2

Select Auto Annotate.

3

Choose one of the available options:

• Auto Annotate Features

• Auto Annotate Parts

• Auto Annotate Primers

4

Upload your reference CSV or ApE file when prompted, or select an already-uploaded file.

5

Labii will automatically scan the sequence and apply annotations based on matches.

6

Review the highlighted features in the sequence map and adjust manually if needed.

Sequence Alignment

Sequence alignment is the process of arranging DNA, RNA, or protein sequences to highlight regions of similarity. These similarities may indicate functional, structural, or evolutionary relationships.

How to Perform Alignment:

1

In the OVE toolbar, click the Alignment icon.

2

Provide the following information in the dialog:

• Alignment Name

• Sequence Name

• Sequence (paste the sequence to compare against the current one)

• Reverse (choose whether to reverse-complement the sequence)

3

Click Submit.

The alignment panel will appear automatically, displaying the alignment. Results are saved by default without any extra steps.

Viewing and Managing Alignments

• Fullscreen View: Right-click the alignment panel and select the fullscreen option for better visibility.

• Delete an Alignment: Close the alignment panel, then click the Save button on the OVE menu bar. Closing the panel followed by saving will remove the alignment from the record.