1. (15pts) Problem 2.4 b, d, and e of the textbook.
2. (10pts) a) Using the Needleman and Wunsch dynamic programming method, construct the partial alignment score table for the following two sequences, using the following scoring parameters: match score = +1, mismatch score = 0, gap penalty = -1. A worksheet containing half of the problem solved is posted to give you a good jump start.
TGTACGGCTATA
TCCGCCTTA
3. (10pts) Problem 2.6 of the textbook.
4. (10pts) a) Using the Smith-Waterman method, construct the partial alignment
scoring table for a local alignment of the following two sequences:
ACGTATCGC
GATGCT
Assuming the match, mismatch, and gap scores are 1, -1, and -1, respectively.
b) Use the table to find the local sequence alignment.5. (10pts) For the two sequences, TACAGATC and TGCACATC, construct a
dot plot using the following two different approaches.
a) Use the simple technique, i.e., place a dot in the plot for each identical pair of nucleotides:
b) Use a sliding window of size 3 and a similarity cutoff of 2 nucleotides.
6. (5pts) Explain how a dot plot can be used to find subsequences of a sequence p that also exist reversely in another sequence q. Draw a picture to show how the dot plot might look like if such substrings exist?
(Exercise: Work on Problems 2.5 and 2.7 of the textbook.)