You can annotate DNA sequence by selecting the required section of sequence and pressing the 'Annotate' button. Annotations are displayed on the graphic maps, and can also be displayed under the DNA sequence by pressing the 'Draw Annotations' button.
On the 'Features' map, you can click an annotation to bring up a menu of options, allowing you to 'Edit', 'Delete', 'Select', 'Colour', 'Hide', 'Highlight' or 'Set as ORF'
If you set a 'Colour' for an annotation, as well as colouring the 'Features' map, you can 'Ctrl' click or 'Shift' click the 'Draw Annotations' button to colour or shade the corresponding DNA sequence for all annotations, respectively.
In the annotation editor/creator, you can set a 'type' eg 'promoter', and then use the 'Features' map 'Options' - 'Open Annotation filter' to display annotations of a certain combination of types only.
You can also set annotations as a 'CDS' (coding sequencing), and check the 'Display All CDSs' options in translated mode to displays a translation of all CDS annotations
Annotations can represent 'joined' ie spliced sequences, like a genbank record 'joined' entry
You can set an annotation as an MCS (Multiple Cloning Site). MCS annotations have special displays in the 'Map', 'Circular Map', and 'Construct Maker' functions
Annotations are also displayed in other parts of the software, such as alignments, primer3 interface, and circular maps
Similar to 'Annotations' are 'Vector Elements' - which were originally used in DNADynamo to describe DNA sequences that had been set as 'circular', (ie Vectors). However, in current versions of the software you can just use the 'Annotate' features without using the 'Vector Elements' if you want as they are now essentially interchangeable.
With Vector Elements you set a 'Catagory' eg 'Promoter', and a Value 'eg CMV' On circular maps, you can opt not to display 'Annotations', and only display 'Vector Elements' - so you could use annotations as a way to annotate vector sequences without the annotations displaying on circular maps.
When you import sequences from genbank, 'features' in the genbank record are converted to annotations. A quick way to annotate a sequence is a BLAST search, then import the corresponding hit/record via the BLAST interface.
When you set a sequence as 'Circular' you can auto-search against an internal database of sequences commonly found in Vectors, and import these as 'Vector Elements'