.
Go to the alignment server at http://www.cmb.usc.edu and
perform local sequence alignment of the following two sequences:
>sequence1
TCAGTTGCCAAACCCGCT
>sequence2
AGGGTTGACATCCGTTTT
a. First set alpha = beta = 1000, and perform the alignment using the
Single score option, with Match score = 10, and with Mismatch Penalty
score = 10, 7, 5, or 3. Observe the effect of reducing the Penalty score by
examining the ten highest-scoring alignments for each case. What trend
do you observe? Explain this trend.
b. Now with Match score = 10 and Mismatch Penalty score = 10, explore
the effect of changing alpha from 15 to 10, and then to 5 (holding beta at
the default setting of 3). What trend do you observe? Explain this trend.