Although the sequence editor is ideal for manipulating sequences and displaying alignments, there is often a need to display formatted sequences including translations and restriction sites. This can be done by creating a features object in the notebook.

1. Open the DNA sequence file pBR322.
2. Select nucleotides 1 through 150 and Copy them to the clipboard by choosing Edit ➧ Copy. Note that if you select these nucleotides and drag them to the notebook, the sequence itself will be placed in the notebook as text.
3. Bring the Untitled GI Notebook window to the fronta by clicking on it or choosing Window ➧ Untitled.
4. Paste the DNA sequence into the notebook (Edit ➧ Paste). This creates a new notebook object called a Features object.b
5. Double-click on the new features object to target it. You will see the appearance of a new Feature s menu added at the right.
6. Select nucleotides 18 through 96 and then choose Features ➧ Define Intron. The selected segment of DNA is displayed in inverse colors to indicate that it is an intronc.
7. Select the entire DNA sequence from 1 through 150 and then translate it by choosing Features ➧ Translate.... When asked for a translation table, choose the E. coli translation table.
8. Choose Features ➧ Adjust Size To Contents to force the size of the object to expand to include all of the DNA sequence as well as the amino acid sequence.
9. Your display should now look like figure like that in Figure 36. Notice how the translation skips over the intron and how, even though the codon is interrupted by the intron, it is reconstructed by the program.

   Figure 36: Features Object with Translation

    

10. We need to adjust the grouping of the DNA sequence characters to align better with the translation. Select nucleotides 1-17 and choose Features ➧ Grouping ➧ Groups Of Three. Notice how the intron grouping is adjusted to remain in groups of ten, but now the grouping starts with the first character of the intron.
11. Select nucleotides 98-150 (in the second "exon") and group it by threes as you did in the previous step.
12. Select the peptide sequence by clicking on it once. Using the Format menu, change the peptide sequence to Arial 9 point italic and color it red. Notice that the numbering style is set to match the actual peptide sequence. This is the only way the peptide numbering style can be changed.
13. Now let's add some restriction site markers. Choose Features ➧ Mark Sites.... Select the Commercial_4 enzyme list and move the first six enzymes in the list (all start with `A') to the right hand Sites to Mark list by pressing the Move >> button. Your dialog box should look like Figure 37. Press Find to mark all sites for the enzymes you have selected.

    Figure 37: Features - Mark Sites

     

14. Select one of the site markers by clicking on it once. Choose Edit ➧ Select All to select all the site markers. Using the Format menu, change the selected site marker text to Times 10 point bold and color blue.
15. Choose Features ➧ Adjust Size To Contents to expand the features object again. You should now have something that looks like Figure 38.

    Figure 38: Features object - Completed

     

16. Try using some of the other options in the Features menu to adjust the display to look exactly the way you want it to. You might select the Box Around style to highlight a specific segment or use the Upper Case or Lower Case styles to indicate other features.
17. Let's take a look at a features object containing a multiple sequence alignment. Open the peptide sequence file called rhodopsins . Choose Sequence ➧ Display ➧ Hide Overview. Align all the sequences by Choosing Sequence ➧ Alignment ➧ Align All Sequences... and perform the alignment with the BLOSUM30 table. Use the Sequence ➧ Consensus ➧ menu to show the consensus row and to show the scoring row.
18. Now click on one of the names in the left column of the sequence window and then choose Edit ➧ Select All to select all the sequences. Make sure you have an open notebook window visible and then drag the sequences from the sequence editor window into the notebook with the mouse. A features object will appear in the notebook with the same alignment as you saw in the sequence editor window.
19. Double-click on the new features object and a Sequences menu will appear. You may use the items in this menu to alter the display of the aligned sequences in this window. Note, however, that you cannot perform any new alignments within this object. It is for displaying the results only. To perform a new alignment you must start from the sequence editor window or else perform a multiple sequence alignment from the Analysis menu.

This concludes this tutorial. You may quit or continue on to the next tutorial. If you choose to continue, close all open windows now.