Editing a sequence

Editing a sequence is as simple as clicking on the sequence within the sequence library. What you can see by opening a sequence, is a circular view of the plasmid, along with a rendering of its annotations and their names. This view here is what we call the map view, and the panel on the right is the sequence view. If you've used DNA editing software before, this should look pretty familiar.

We can select portions of the sequence in either the map or the sequence view, just by clicking and dragging. By default, selections lock to the starts or ends of annotations in the map view, but you can select any sequence by holding control while you select, or you can select in the sequence view. You can fine-tune selections by dragging the edges of the selection in the sequence view.

By default, vector editor only displays features and their labels, but this can be changed in the view menu. In the view menu, you can toggle display of features, restriction enzyme cut sites, and ORFs. You can also toggle the display of amino acid sequences in the sequence view. There are shortcuts to display features, cut sites, and ORFs in the toolbar as well.

You'll notice that mousing over features, cut sites, ORFs, or their labels will give you a more detailed description of them, and clicking them causes their positions in the sequence to be selected.

You can also toggle whether we want the sequence to be linear or circular, or you can reset the first basepair of the sequence using 'rotate to here.' This will change the origin of the sequence to be the location of the cursor.

You can search within the DNA or Amino Acid sequence, using either literal search, which only allows a's, t's, c's, or g's for DNA search and amino acid letters for amino acid search, or ambiguous, which allows characters like n to represent all the bases, and so on.

Creating and editing a sequence feature

If you want to create a new feature, select a portion of the sequence, and right click on your selection. Clicking the 'annotate as new sequence feature' option will bring up a window allowing you to specify the name and location of the feature, as well any additional attributes you want it to have. You can also change the feature’s type. This is an attribute with a number of different options that describes the feature’s function.

Features can also be edited by right clicking on them and selecting the 'edit sequence feature' option. You can modify their name, type, location, etc.