Contents of this Article
The Open Vector Editor
The Open Vector Editor (OVE) is a user-friendly open-source tool that can be used 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:
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. 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.
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.
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
Edit locks
Find tool
On the lower part, the software indicates the length of your sequence and the amount of bp selected if that is the case.
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. In some cases (like in the image shown) there is a warning icon indicating there is something wrong with the view. In this case, not all the cut sites are shown since the total amount is higher than the limit established.
On the left side, you can see the sequence map. 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).
