Plasmid Editor
A comprehensive tool for managing plasmid constructs
Overview
The Labii Plasmid Editor widget is a comprehensive tool for managing plasmid constructs within Labii’s ELN and LIMS platform. It allows users to view and edit plasmid sequences, as well as add, modify, and annotate genetic features such as promoters, genes, restriction sites, and origins of replication. With an interactive graphical plasmid map and a synchronized sequence viewer, users can seamlessly edit both the visual and text-based representation of the plasmid. This widget streamlines the design, documentation, and sharing of plasmid constructs, making it ideal for molecular cloning, synthetic biology, and genetic engineering workflows.
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.
Interface
Labii's Plasmid Editor has a menu bar, a main body (views), and a status message.
Menu bar
The menu bar includes all the functions necessary to modify the plasmid sequences and features. Each function is represented by an icon, and when your mouse is hovered over the icon, the tool's name is displayed. A menu bar can be seen only in edit mode and hidden in read-only mode.
The menu bar contains the following tools:
Views - Switch to a different view. Default to Both Flip
Open - Load data from a file
Load from accession - Load data from an NCBI accession ID or iGEM part ID
Search - Search function
Rename - Rename the plasmid
Add enzymes - Add enzymes to see the digest results
Zoom in
Zoom out
Uppercase - Change all sequences to uppercase
Lowercase - Change all sequences to lower case
Show/Hide complement
Show/Hide axis
Status
The left side of the status message shows the metadata of the selection. Specifically, the start and end positions, the length of the selection, the TM and the GC.
The right side of the status message shows the percentage of zoom
Views
Plasmid Editor provides various views to help you understand plasmid sequences and maps. Click the "Views" menu in the menu bar to switch views.
Both
The Both View displays both a linear and circular viewer. The Both View shows the circular viewer on the left and the linear viewer on the right. In Both Flip View, the linear viewer is on the left, while the circular viewer is on the right.
Linear
In the linear viewer, DNA sequences are displayed alongside features and axes. Zooming out allows you to see just features.
Circular
The circular view displays the plasmid map.
Features
Feature views show a list of features annotated to plasmid sequences. Other tools in the menu bar can be used to add, edit, or remove features. There are the following columns in the features table:
Name - The name of the feature. Highlighting the name text with the feature's color.
Type - The type of the feature.
Start - The start position of the feature.
End - The end position of the feature
Direction - The direction of the feature. 1 as Forward, -1 as Reverse
Enzymes
On the enzymes view, you can see the digest enzymes used and their cut sites. The "Add enzymes" tool can be used to add, edit, or remove enzymes. It contains the following columns:
Enzymes - The name of an enzyme
Recognition site sequence - The enzyme recognition site sequence. The highlighted nucleotides indicate the position of the cut.
Cut sites - Position of the enzyme cut sites on the current plasmid. Multiple numbers indicate multiple cuts. An empty value indicates no enzyme cut sites.
Load from a file
Data from an external plasmid file can be loaded into Labii Plasmid Editor. To do that:
Choose a file by clicking "Open" in the menu bar.
Or
Drag the file to the "cloud" icon. You can also select a file by clicking the "cloud" icon.
Supported file format:
*.gb or *.gbk, NCBI GeneBank file.
*.ab1, AB1 files mostly belong to Sequencing Analysis Software by Applied Biosystems.
*.ape, ApE file.
*.fasta or *.fas, a text-based format for representing either nucleotide sequences or amino acid sequences.
*.json, JSON file exported from Benchling Molecular Biology Suite.
*.xml, iGEM BioBrick file.
*.seq, plain text files containing your sequence in FASTA format.
*.sbd, sequence builder file.
*.dna, SnapGene file.
Search
A sequence can be searched within a plasmid. You can use the search function to find the position of a given sequence. For instance, you can add a primer to the plasmid by searching for the primer's position and then clicking on "Add feature".
To conduct the search:
Click the "Search" in the menu bar
Provide a sequence to search in the Query field. The wildcards of the following can be used:
y: c, t
r: a, g
w: a, t
s: c, g
k: g, t
m: a, c
d: a, g, t
v: a, c, g
h: a, c, t
b: c, g, t
x: a, c, g, t
n: a, c, g, t
Provide the maximum allowable mismatch between the query and a match.
Click Submit
The search results will be highlighted in yellow.
Change bases
Plasmid Editor allows the modification of Plasmid sequences.
To insert bases, click the position you wish to insert in the linear viewer, and then click "Insert bases at selection". Type or paste the nucleotides into the pop-out modal. Press Submit to submit.
The bases can be modified by selecting the sequences and clicking "Edit selection bases" in the menu bar. This will display the selected sequences in the pop-up modal. Make any changes and click Submit.
To delete selection bases, select the sequences and click "Delete selection bases".
You can copy selected bases by selecting the sequences and clicking "Copy selection bases".
Change features
You can also add, edit, and delete features.
In the menu bar, click "Add feature" and provide the Name, Type, Start position, End position, Direction, and Color. When you're done, click Submit. In addition, you can also select a feature in the linear view and click "Add feature", the start and end positions will be automatically filled in the feature form.
If you wish to edit a feature, select it and click "Edit this feature". Edit as necessary, then click "Submit".
You can delete a feature by selecting it and clicking "Delete feature".
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