Contents of this Article
The Open Vector Editor
The Open Vector Editor (OVE) is a user-friendly open-source tool to view, design, edit, and annotate plasmids and their sequences. When you open a DNA part or sequence from your library, this is the typical view you obtain of the OVE:
This shows you two different views of your DNA sequence: a plasmid view on the left side and a sequence view on the side part. Selecting one sequence segment on one side will automatically select it on the other. In this article, we will see all the visible features and options you can find on a sequence on the OVE (to better understand the options to directly work with sequences there, go to this article instead).
The Upper Menu
On the upper part, there is a set of options that includes:
File: Includes options to add a new sequence, or rename, delete, save, duplicate, export, and print the one you are working on. Here, you will see the option to activate the Read Only Mode (option only available for admin users). It also includes the option “Properties” that opens your sequence properties on the right side of the screen.
Edit: Includes some options to edit your sequence. Most of the options on this menu are also available using keyboard shortcuts.
Change case to see capital/lowercase letters, change between a circular or linear view, and change a selected segment of the sequence for its complementary basepairs by clicking on “Complement Section”
Obtain the complementary bp for the whole sequence by clicking on “Complement Entire Sequence”. This can be undone by ctrl/cmd + z, or by clicking on “Reverse Complement Section”, or “Reverse Complement Entire Sequence”.
View: Allows you to activate or deactivate the view of several features: primers, parts, cut sites, ORFs, colors to indicate DNA bases/amino acids, labels, etc.
Tools: The available tools to work with the OVE are: filter cut sites, manage enzymes, create custom enzymes, simulate digestion, simulate PCR, remove duplicates, and auto-annotate. Click here to learn more about OVE's tools, and the DNA auto-annotation process.
Help: It includes information about the OVE and hotkeys.
Notice that, in the upper right corner, there is an option to duplicate the sequence and open it on its corresponding library.
General Display
Under the upper menu of the OVE, you will find the following icons:
Export
Undo
Redo
Hide/show cut sites
Hide/show features
Hide/show parts
Hide/show primers
Hide/show ORFs
Align to the sequence
Enable/disable editing of the sequence (admin-only option)
Find tool
On the lower part, the software indicates the length of your sequence and the amount of bp selected (when applicable). It also gives you the GC% and the option to select the inverse sequence.
On the right side of the screen, you have the plasmid or linear map of your sequence. The view will depend on the features you decide to show or hide. On the left side, you can see the sequence map.
In some cases you may see a warning icon indicating there is something wrong with the view (for example, when not all the cut sites are shown since the total amount is higher than the limit established). Similar to the plasmid view, the amount of visible features will depend on your preferences:
Notice that some sequences can be displayed with base pairs or amino acids, with or without color codes.
Adding Sequences
To add a new sequence and work on it on the OVE, you can select “New Sequence” from the “File” option of the upper menu and fill in the required information:
Once your new sequence is created, a blank display will appear, where you can paste your sequence:
Another way to import a new sequence is directly uploading it to your library, by clicking on the “New” icon (the information required will depend on the library you are using).
