Dynamic programming by hand - fun and easy!

For the following exercises all you will need are pad and paper. You will make three different alignments of two amino acid sequences that are only two residues long each: WK and RF. You will do a global alignment twice with two different linear gap-penalties, and you will do one local alignment. To do these exercises you will need to know the match/mismatch scores for all 4 possible amino acid match-ups, and you will need to know the gap penalty. Here are the mismatch scores, taken from the BLOSSUM 50 matrix:

	W	K
R	-3	3
F	1	-4

For each exercise you'll want to draw out a table that looks like this:

		W	K
	0
R
F

You will then fill out this table according to the Needleman-Wunsch or Smith-Waterman algorithms using the score matrix above and the given gap penalty. At the end you will have a full table and a corresponding traceback path, from which you can write down the corresponding alignment. Write down the alignment and its corresponding score, which is the number at the beginning of the traceback path.

Please try the following:

1. Global alignment with gap penalty -8.
   
   
2. Global alignment with gap penalty -4.
   
   
3. Local alignment with gap penalty -4.
   
   

Write down your answers and scores, they will be announced at the end of the class.