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1. Start GCK and open the file construct#4 from the tutorials folder we provided.
2. It is possible to modify the sequence appearance using many of the items in the Format menu. Select the AT-rich segment from nucleotides 10-33 by dragging with the mouse. Now Choose Format > Font > Times and notice that even though Times is not a monospaced font, GCK still spaces the characters uniformly. Now choose Format > Style > Bold. The bold characters are wider than the non-bold characters so this part of the sequence becomes more spread out. You can adjust for that by choosing Format > Style > Condense.
3. Another method can be used to illustrate features -- Frames. To see how frames work, select nucleotides 676-699 and choose Construct > Features > Make Frame. This will create a frame around the selected segment of DNA and will include the region (amino acid sequence) and site markers. It should look similar Figure 19. The frame is selected (highlighted) and encloses all information related to that particular segment of DNA.
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Figure 19: A Framed Sequence
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4. The appearance of the frame can be altered by using items in the Format menu, as usual. Note that a frame must be selected in order for items in the Format menu to have any effect on the frame itself. With the frame selected, choose Format > Lines > and choose the second line thickness in the menu. Choose Format > Color > Yellow, and then choose a fill pattern using Format > Fill. You can try different patterns and colors to see how they look.
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Figure 20: Set Frame Contents
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5. You can limit what is enclosed in the frame by choosing Construct > Features > Set Frame Contents... as shown in Figure 20. This dialog allows you to define which items will be enclosed in the frame. Set your dialog box to look like the one shown here and then press OK.
6. It is somewhat difficult to distinguish between the DNA sequence and the protein sequence, so let's change the appearance of the protein sequence. Click once to select the protein sequence and then choose Format > Font > Times, then Format > Style > Italic. Your display should now resemble that shown in Figure 21. The ability to alter the display of the sequence in so many ways provides a great deal of flexibility in pointing out specific features of any sequence with which you are working.
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Figure 21: A Modified Framed Sequence
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7. Choose Construct > Display > Display Graphics. Note that the new region you defined as the origin of replication also appears in the graphical display. There is a direct correspondence between the two views of the construct. Changes you make in the graphical view appear in the sequence view and vice versa. The graphical view represents an easier way to visualize your construct.
8. Click on the BamHI site marker name and then select all site markers by choosing Edit > Select All. We want to change the appearance of all the site markers except for the BamHI site so we need to deselect only the BamHI site. This is done in the standard way by holding down the shift key and clicking on the BamHI site (called shift-clicking). Now choose Format > Site Markers > Show Site As Symbol. You see something like Figure 22. Note that you might have different symbols.
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Figure 22: Sites Marked as Symbols
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