Discuss the limitations of the Nussinov algorithm for RNA folding prediction
Discuss the use of clustering in the analysis of gene expression microarray data
March 21, 2023Describe the differences in complexity and usage between hierarchical clustering and the Markov clustering (MCL) algorithm
March 21, 2023Discuss the limitations of the Nussinov algorithm for RNA folding prediction
COMPUTER SCIENCE TRIPOS Part II – 2015 – Paper 9
Bioinformatics (PL)
(a) Define the Longest Common Subsequence (LCS) problem between two strings
and find a solution for the case of the two strings:
ACGT and GGTTTAAGCCGT
[4 marks]
(b) Discuss the limitations of the Nussinov algorithm for RNA folding prediction.
[4 marks]
(c) Which algorithm would you choose for clustering sequence and gene expression
datasets and why? [3 marks]
(d) Discuss the complexity of the Markov Clustering (MCL) algorithm. [4 marks]
(e) Discuss the assumptions for the use of the Gillespie algorithm in the study of
reaction networks and comment on the algorithm’s complexity in terms of the
number of reactions. [5 marks
