Assignment/Class Test
1. You are given two DNA sequences to align ACGTCCTTCATT and GTCTCATG
You have a scoring scheme where a
• match gives you +1
• a mismatch gives you 0
• gap opening costs −10
2. Write down the best alignment of the two sequences
You have a scoring scheme where
• A match gives you +1
• a mismatch gives you −1
• opening a gap costs you −1
Write down the best alignment for the same two DNA sequences.
3. You have calculated a score matrix for a pair of DNA sequences. You have performed
the traceback calculation and found a result like:
Write down the corresponding sequence alignment with gaps in the correct positions.
4. Use global dynamic programming to align the following two sequences. Fill the matrix
and write down an optimal alignment.
Scoring function: S(match) = 2, S(mismatch) = -1, S(gap, character) = -2
5. Describe two main differences between local dynamic programming algorithm (Smith-
Waterman algorithm) and global dynamic programming algorithm (Needleman-Wunsch
algorithm).
6. For the scoring matrix BLOSUM62, what does “62” stand for? List one difference
between the process of constructing BLOSUM matrix and PAM matrix.
7. For the following pairwise alignment, calculate the similarity score, using
theBLOSUM45 scoring matrix provided.
AB017061_16 V M S K V R E M P
VAC027034_19 A L S E V R E M P
