Open Vector Editor

Design DNA and protein sequence

Overview

Plasmid a genetic structure in a cell that can replicate independently of the chromosomes, typically a small circular DNA strand in the cytoplasm of a bacterium or protozoan. Plasmids are much used in the laboratory manipulation of genes.

Biotech scientists need to deal with plasmid almost everyday in their Electronic Lab Notebook (ELN) and Laboratory Information Management System (LIMS), Labii ELN & LIMS is now providing plasmid related functions to facilitate research.

Labii currently provide these widgets:

Category

Widget

Type

Description

Molecular Biology Suite

Files, File, Files (No Preview)

Section

View map of a plasmid

Molecular Biology Suite

Open Vector Editor

Section

Build / Edit plasmid map

Plasmid Viewer

Use the widget (Files, File, Files (No Preview)) to display the map of a *.gb in circular or linear format. GenBank (*.gb) is a plaintext format for storing DNA data as character sequences. Read here for more details.

To view the map, upload a file (*.gb, *.gbk, *.ape) and the plasmid will show automatically.

Open Vector Editor

Open Vector Editor is originally designed by Teselagen. A widget is created in Labii ELN & LIMS to enable you to:

  • See the sequence of a feature

  • Update the sequence of a feature

  • Manage all properties

  • Manage primers

  • Manage protein translations

  • Manage cut sites

  • Manage ORFs

Open Vector Editor

How to use

To use this function, follow these steps:

  • Add a section with widget Open Vector Editor

  • Paste sequences or import sequence from a *.gb, *.ape, etc.

  • Add or change features. Left panel shows the Circular or Linear Map, the right panels shows the Text Map. Text map shows DNA sequence, translation, and features as text-based graphics.

  • Click Fullscreen to view the editor at full screen

  • Click Standalone to view the editor in a standalone view. The Standalone view will only show this widget and provide all space to working on the widget.

Import sequence

Sequence can be create via importing *.gb, *.gbk, *.ape files.

To do that: File -> Import sequence

Export sequence

Sequence can be exported from File -> Export sequences

This supports:

  • Genebank File

  • Fastq file

  • Teselagen JSON file

Edit sequence features

Add a plasmid editor widget and you can starting load sequence and see the features at the real time. All the feature will be loaded automatically and the sequence can be changed on the right side of the panel.

Select a sequence and right click to change / delete / create a feature.

All features are summarized in the tab of Features. You have the option to change the color, name, type, strand.

To reach that:

  1. Click the Properties on the right side panel

  2. Click Features

  3. Select a feature

  4. Click New to create a new feature

  5. Click Edit to edit the current selected feature

  6. Click Delete to remove a feature

Manage cut sites

All cut sites will be listed under Cutsites. See the picture bellow.

Virtual Digest

The size of the DNA fragment can be viewed at the virtual digest.

Virtual Digest