COMPUTER SCIENCE TRIPOS Part II – 2013 – Paper 7
Bioinformatics (PL)
Given the two DNA sequences: GCACTT and CCCAAT
(a) Compute the alignment (using the edit graph) and the final score with the
following rules: match score = +1, mismatch = −1, gap penalty = −1.
[4 marks]
(b) Discuss how the alignment score and the quality of the result depend on the
match score, mismatch, and gap penalty. [6 marks]
(c) Generate four, short DNA sequences (a,b,c,d) such that their relations as a tree
are approximately the following: ((a,b),(c,d)). [5 marks]
(d) How is the score matrix used in phylogenetic tree building techniques?
[5 marks]