In order to complete this practical your computer must be connected to the internet as the software retrieves database entries from the sequence repositories at the European Bioinformatics Institute UK.

Retrieve the sequence af361440 together with its feature table using the same method as described in the Input-Output Tutorial. Double click on the saved file in the file manager and scroll down to the features for the complete coding sequence of the cloning vector pBT.

If you do not want to run through this tutorial it does not matter. It just means you will not have the sequence to compare the features - you'll just have to take our word for it!

Open the DNA editor by selecting it from the Jemboss Tools menu. Hit the OK button to accept the default to Create new DNA display.

Accepting to create a new DNA display will open the DNA Wizard. This wizard offers all the possibilities for creating a graphical representation in one simple form. Once the display is complete, individual features may be accessed from different forms in the DNA Viewer menu. Using the feature table retrieved from the full EMBL entry of the CCR5 complete coding sequence (CDS), an authentic representation of the genetic features in this sequence can be made.

In the DNA Attributes section of the wizard, on the left hand side, leave the default Circular selection.

Leave 0 in the Start box and type 3209 into the Stop field. Alter the Line Width to 5 either by typing the number in the box, or sliding the rule bar to the left until the number 5 is shown. Hit the OK button to create the initial graphic.

Access the Options menu on the DNA Editor and select Tick Marks. To the right hand side of the attributes list, alter the Tick Interval to 500 and the Minor Tick Interval to 10 by deleting the text in each input box and typing in the relevant figure. Leave the Start Tick as 0. Hit the Set button and the tick marks in the graphic will represent the new values.

The resulting graphic should be a circular display numbered every 500 bases with minor ticks at intervals of 10 bases. The default numbering for the begining of a sequence is 0 - which is equivalent to the first base. To be entirely correct about positioning, 1 has been deducted off each feature position to take this into account. This is not strictly necessary unless you are working with a very short sequence and a difference of one will be obvious in the graphic.

Select Genetic Markers from the Options menu. Type 1555 and 1585 into the Start and Stop positions respectively. Alter the Line Width to 8 and hit the Add Marker button. The label appears in the upper table.

Each Marker that is added is labelled by default as "CDS" and coloured red. It also displays an arrow head to indicate direction and this can be seen on the circular graphic. The absence of any line with this arrow is due to the relatively small size of the feature. It is slightly wider than the plasmid representation due to the larger line width.

Position the mouse over the CDS label box and click once to access the text in the box. Delete this label and type lacUV5 to represent the promotor into the box instead. Hit the enter key on the computer to confirm the choice.

Click on the colour swatch to display alternative colour options. Select a dark blue option from the left hand side of the Swatches options. Hit OK to confirm the choice and your selection will be transferred to the display.

The colour options can be customised in a variety of ways. Instead of selecting a shade from the swatches, the RGB or HSB selections can be used. This allows a precise colour to be reproduced if necesssary. The arrow markers are designed to speccify direction, and the head is selected as default as it is often the case that feature direction is on the forward strand. Should you need to reverse the sense, simply replace the arrow head with the tail.

Add a second feature (Multiple Cloning Site) at position 2341 to 2393. This feature has no direction atttributed to it. Colour it green and specify the line width as 8.

Two possibly siginificant features have now been added to the representation of the pBT cloning vector. Colouring can obviously be used more sensitively depending on the display.

Enter the two coding sequence features. The first is at 1 to 219 on the forward strand, and the second at 2770 to 3210 on the complement strand. Remember to deduct one base off the end of each postion to allow for the initial start at 0. Pick any colour you like.

The display should now contain all four features, with the two coding sequences going in opposite directions.

Access the results from the Parameter Tutorial to note the site for the unique cutter NotI at position 2344. There is also a BglII site at position 2389.

Open the Restriction Enzyme window from the Options menu. Type NotI into the Label input box and enter its Position as 2343. Hit the Add RE button.

Alter the colour to dark green by selecting the red swatch and choosing from the appropriate palette.

Repeat with the BglII site at the opposite end of the multiple cloning region.

The final display should show the entire cloning vector complete with all represented features.

There are endless possibilities to create both circular and linear graphics using the DNA Editor and adding various restriction sites and genetic features. These can be saved as an image or printed straight out as hardcopy.