How to use Plasmid Map Editor? - LabCollector

Search Knowledge Base by Keyword

You are here:
← All Topics

Inside LabCollector  there are 13 by default modules, amongst which you can find the Plasmids module

This module not only offers you the possibility to import plasmids, but also create your own ones with the help of the Plasmid Map Editor. But in order to access this feature and be able to create your plasmids, you will need to follow the below steps.

In Plasmid Map Editor, you have two options to generate a plasmid, either you make one by modifying a base design (to use this feature, all you need to do is click on ), or create one from scratch by importing its corresponding DNA sequence (to use this feature, you need to click on ).
1. Design mode
2. Draw from sequence

1. Design mode



  • You can also edit an already existing plasmid record by clicking on it and then selecting the ‘Sequence and map‘ option.



  • Once done, you will see the below page.

  • 1. Here you can input the plasmid’s name and its size in base pairs (bp). You can also zoom in and out of the plasmid with the ‘radius‘ option.
  • 2. This area gives you a preview of how your plasmid looks like while editing it.
  • 3. Features section allows you to add, for example, an ORF (Open Reading Frame), an ORI (Origin of Replication) or an antibiotic (tetracycline, ampicillin, etc.). Below is a screenshot with an example of some features that you can add.

You won’t be able to visualize the feature unless you click on button.
  • 4. Here you can input “Additional Annotations“, such as the coding sequences (CDS) or primer binding sites. You can also add any other additional annotation that you require. Below is a screenshot with an example of some annotations that you can add.
  • 5. GenBank Annotations allows you to add annotations directly from GenBank. For example, let’s say you have downloaded a plasmid file from GenBank and uploaded it into the plasmid module. If you want to add the same annotations as the ones present in GenBank, you can then choose to visualize and add them into your plasmid by ticking the “Include GenBank annotations” box.
  • 6. You can also add Restriction sites to your plasmid. See screenshot below for an example.

  • 7. Once finished, you can save your plasmid by clicking the save button after giving it a name, and it will automatically get added into the plasmids module.
If you want to see or add annotations in a particular plasmid record, you will need to click on Manage Sequence & Annotations. (See screenshot below).

2. Draw from sequence

  • Once inside the Plasmid Map Editor, click on located at the top. You will then see the below page.


  • 1. Here you can copy-paste the DNA sequence that correponds to the plasmid you want to generate (as shown in the screenshot above).
Please note that this import process will detect ORFs with orientation and commercial restriction enzymes positions. Common selection markers will also be identified (e.g. Ampicilin).
  • 2. Here you have a list of all available enzymes (to the left) and another tab located to the right for the restriction enzymes you are going to use when importing your DNA sequence.
    • You can select an enzyme from the left tab and click on the Add button to add it to the list of enzymes you are willing to use, and you can also remove the ones that are ready for use, by selecting them then clicking on the remove button , they will then get automatically transfered back to the list of available enzymes.
  • 3. Here you have a table with a list of different genetic codes that you can select, depending on the codon table and type of species you are working with. (See screenshot below for the full list of codon tables that you can use).

  • 4Once finished, click on the “Import and draw!” button to view your plasmid (below is an example of a plasmid generated based on its DNA sequence).

Please note that you can always change the plamid’s name, add/remove annotations and restriction sites after it was generated.

Related topics: