In addition to storing and displaying sequences, the sequence editor is also a convenient place from which to launch multiple sequence alignments and to fine tune the alignments once they are generated. Multiple sequence alignments can also be created as a new analysis. In this tutorial, we focus on performing multiple sequence alignments directly within the sequence editor document.

1. Open the peptide sequence file called “rhodopsins”.
2. Choose Sequence ➧ Alignment ➧ Align All Sequences…(a). This will bring up Figure 17. The parameters displayed in this dialog are described in more detail elsewhere and represent values needed by the algorithm to perform the alignment. For now choose the BLOSUM62 table and leave all the parameters at their default values. The analysis table is chosen using a popup menu. Press and hold the mouse button down on the word None next to the word Table: at the top left of the analysis panel. This will cause the appearance of a popup menu. Choose Standard ➧ BLOSUM62.
3. Press the Align button to start the process of aligning all the sequences in the document. Progress is indicated in the upper left corner of the sequence window, just above the column of sequence names.
4. After the alignment is complete, you will see the sequences aligned in the sequence document window. Our goal will be to use the Gene Inspector features to change the view to look like that shown in Figure 18.
5. Choose Sequence ➧ Display ➧ Hide Overview. This will hide the overview “pane” at the top of the sequence window which is no longer helpful because all sequences being displayed are now the same length.

   Figure 18: Aligned Sequences

6. Choose Sequence ➧ Consensus ➧ Show Consensus Row. This will add a new row above the sequences showing the consensus sequence – the most common character in that particular position of the alignment.
7. Choose Sequence ➧ Consensus ➧ Show Scoring Row. This will add a row containing a histogram indicating how good the match is at each position.
8. Finally, choose Sequence ➧ Consensus ➧ Show Shading. This will add shading to the document which should now look similar to Figure 18. The shading indicates which residues match the consensus sequence residue. The more residues that match the consensus residue, the more intense the shading will be.
9. Click on the word “SCORE” in the name column to select the entire scoring row. Try choosing different colors and patterns using the Format menu. Notice how the shading changes to reflect your choices.
10. You can also choose to place custom adornments on the aligned sequences. Choose Sequence ➧ Consensus ➧ Custom Score Adornments…. and try some of the options for depicting the aligned sequences in the exact arrangement you want.
11. Choose Sequence ➧ Consensus ➧ Automatic Updating. This instructs Gene Inspector to automatically update the score (top left corner of the window) each time you edit one or more of the sequences. Note that this does not automatically realign the sequences, it just updates the score. Automatic updating places some demands on the computer, so it might slow down your typing if you are using an older (slower) computer.
12. Try editing the sequences to see if you can increase the score. The Clustal algorithm is quite good and it will be difficult to better the alignment generated by the algorithm.

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