1. Find the best global alignment of the following sequences using the Needleman Wunsch algorithm. Show the tabular and trace-back matrices. Assign +2 for matches, -1 for mismatches and -2 for gap penalty. What is the score of the alignment?
S1: ACGTCATCA
S2: TAGTGTCA
1.a How many global alignment are possible for these two sequences?
1.b How many global alignments generate the same maximum score?
1.c Find the best local alignment of the sequences in question 1 using the Smith-Waterman algorithm. Use the same scoring system as in question 1 and show the tabular and trace-back matrices.
1.d Create a dot-plot of the two sequences and identify similarities (if any).