Exercise 3: The physical meaning of Q

This exercise will further examine structure conservation. Make sure to change Molecule Coloring back to Q per residue.

1 Go back to the main MultiSeq window top pull-down menu and select Tools $\rightarrow$ Residue Selection. 2 Select Q Value. 3 Select Less than and 0.1 value. 4 Then click on the Select button.

Figure 18: Exercise 3

 
If you had set Molecule Coloring to Q per residue you will notice that the majority of the red areas have turned yellow, and the blue is visible. If you look in the Sequence Display, you will see that the majority of SerRS residues have been highlighted. By using these settings in Q value, you have demonstrated where the aligned molecules have the least structural conservation,Q$\le$0.1.

Figure 19: Q$\le$0.1

Now select Greater than or equal to and 0.6 in the Q Value window , and click on Select. Notice, in the OpenGL Display that the majority of the Blue area inside the molecules has turned yellow. Also, note what has occurred in the sequence display. Many areas of the AspRS molecules are highlighted. Occasionally, an amino acid in SerRS is highlighted along with those of the AspRS. As you increase the value to 0.7, there are no highlighted residues from SerRS. Now that we have completed the exercises in Residue Selection, close the Select window.