In DNADynamo you can set sequences as circular, either by selecting the 'circular' checkbox in the sequence view controls panel,
or with menu option 'Vector' -> 'Set this sequence as circular (a vector)'
following activation of the 'circular' function, you are given the option of auto-finding potential functional elements
within the sequence by comparison to a database of common sequences found in vectors (eg promotors, resistance genes etc).
Found features are displayed on a map, and must be selected by clicking with the mouse, or via the 'select all' option, before 'importing'
You can also import vector sequences from genbank format records - together with the vector features described in the record
Vectors can be annotated either with standard 'annotations' or with 'vector features'.
In current versions of the software these two forms of annotations have essentially the same functionality.
In older version of the software, vectors could only be described with 'vector elements/features'.
Vector Features have a 'catagory' eg promoter and a 'value' eg CMV, as well as a direction and location, while Annotations have a single 'label',
direction and location. You can opt to display only vector features on circular maps
, or include standard annotations as well
You can define 'multiple cloning site' features/annotations - which allows clearer displays or restriction enzyme sites with MCS features on linear and circular maps, and within the construct maker.
DNADynamo will identify restriction sites that cross the notional 'zero' point in the sequence
eg a BamH1 site will be found in the sequence TCCNNNNNNNNNNNNNNNNNNNNGGA if it is set as circular, but not if it is set as linear
restriction sites and annotations/features can be displayed on a circular map
When you save a sequence that has been set as circular, you are given the option to save it in the 'Vectors folder', which by default is the 'Vectors' folder in the DNADynamo installation folder.
The 'Vector Box' folder is the default folder where vectors are looked for in the 'Construct Maker' - though you can also 'change' folders.
You can chnage the location of the default Vector Folder using the menu option 'Vector' -> 'Set default vectors folder location'. For example, you could point the vectors folder to a shared iCloud folder such as DropBox or SkyDrive.