Importing Vectors
You can import vector sequences from genbank format files, or auto-find vector features in a plain DNA sequence.
AutoFind looks for features already described in other
vectors in your 'Vector Folder' and/or in a predefined library of sequences.
You can also manually annotate vectors with 'annotations' and 'vector features'.
Genbank format files are available for many vectors, either in public databases or on vector suppliers web sites.
These files contain the DNA sequence and the location of useful vector features such as Multiple Cloning Sites
(polylinker), antiobiotic resistance genes and promoters.
Note that the 'LOCUS' line in a genbank format record should state whether the record is 'linear' or 'circular', but this isn't always the case. If DNADynamo
can't identify if the record is linear or circular you'll be asked to specify, unless you use a direct 'import vector' option
To import a vector from a genbank format file, either...
a) enter the NCBI accession number (if available) in the 'GO' box, and press the 'GO' button
b) open a saved file containing the genbank format record using 'File' -> 'Open' or 'Vector' -> 'Import vector from genbank format' -> 'Open Genbank format file'
c) 'copy' the entire text of the genbank record and 'paste' the text into a new empty DNADynamo main window (where you would usually paste DNA) - you must copy the entire record -
from the initial 'LOCUS' text that defines the start of the record, to the final '//' characters, that define the end of the sequence
if the genbank record doesn't define a 'multiple cloning site' (MCS) for a sequence, you can add one manually.
The easiest way to do this would be to display
a restriction enzyme map, click the enzymes that define the 5' and 3' ends of the MCS to highlight them on the sequence.
Select the sequence that covers the MCS with the mouse, press the 'Annotate' button, enter 'MCS' as the annotation name,
and check the 'MCS' check box, before saving the annotation (note that the MCS checkbox is only present in the annotation editor
when the sequence is set as 'circular' (a vector))
Additional text and/or image data pertinent to the vector may be saved in the vectors
notes section (accessed by pressing the 'notes' button. eg right click an image on a website, select 'copy image',
then 'paste' the image into the sequences 'notes'
You can manually add annotations to the vector sequence by selecting the required sequence with teh mouse,
and pressing the 'annotate' button, or add 'vector features' via the menu option 'Vector' - 'Add New Vector feature' -> 'select catagory' -> 'select value'.
An example of a DNADynamo 'vector feature' is the ampicillin resistance gene. DNADynamo describes vector features in terms of
a Category (in this case Bacterial Selection) and a Value
(in this case, ampicillin). Other Values in the Category 'Bacterial Selection' might be
Kanamycin and Chloramphenicol. Another example of a Category and Values would be 'Promoter' and 'CMV', 'T7' and 'SV40'.
Each features can be given a location within the Vector Sequence (Start and Stop) and a direction.
Direction are Clockwise (that is 5' to 3'), anticlockwise (that is 3' to 5') and directionless.
When you add 'vector features' - new catagories and values that you use are added to a pre-saved list of catagories and values that you can access next time you add a new features.
You can edit these pre-saved catagories and values (eg delet unwanted ones) via menu option 'Vector' -> 'Edit Saved Catagories and Values'
The amount and extent of the information entered about vectors is entirely up to the user.
Perhaps the most useful 'Vector Element' to add is the Vector Multiple Cloning Site, allowing rapid access to the MCS via the
MCSViewer and in the Virtual Subcloning' tools. In addition, pasting text and images into the notes section is a quick way to record vector
information that may subsequently be recalled while looking through the vector box.
You may add details such as 'Ampicillin Resistance' and 'CMV Promoter' etc without defining exactly the location or direction of the
elements within the Vectors Sequence. These properties would nevertheless be available as a quick reminder when looking through the Vector Box
for a vector with specific properties. If you wish to produce graphic maps of the vector which include the vector elements as well as restriction sites you must
however provide the location information.