Compute the global alignment between the two strings s1 = ACCGTT and s2 = AGTTCA
Discuss, with one example, the complexity of the Nussinov algorithm for RNA folding
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March 21, 2023Compute the global alignment between the two strings s1 = ACCGTT and s2 = AGTTCA
2009 Paper 9 Question 3
Bioinformatics
(a) Compute the global alignment between the two strings s1 = ACCGTT and
s2 = AGTTCA, considering the following scoring parameters: +1 for match,
−1 for mismatch, and −1 for a gap.
(i) What is the maximum similarity score between the two sequences s1 and
s2? [2 marks]
(ii) Find an alignment with this similarity score. [2 marks]
(iii) Is the alignment you found unique, or are there multiple alignments
achieving the maximum similarity score? [1 mark]
(b) Discuss the complexity of the Sankoff parsimony algorithm. [4 marks]
(c) Discuss the main differences between K-means, Superparamagnetic and
Markov clustering algorithms. [7 marks]
(d) Discuss the utility of the Gillespie algorithm in system biology. [4 marks]
