Discuss the use of clustering in the analysis of gene expression microarray data
Explain the steps and the complexity of the Hirschberg algorithm and illustrate them with an example
March 21, 2023Discuss the limitations of the Nussinov algorithm for RNA folding prediction
March 21, 2023Discuss the use of clustering in the analysis of gene expression microarray data
COMPUTER SCIENCE TRIPOS Part II – 2015 – Paper 7
Bioinformatics (PL)
(a) Compute the global alignment and the best score of the following sequences
CGTGAA, GACTTAC with the following parameters: match score = +5,
mismatch score = −3, gap penalty = −4. [4 marks]
(b) If the sequences have different base composition or length, what parameter values
would you choose in order to determine multiple alignment of the sequences?
Justify your answer. [4 marks]
(c) Discuss the main features of the Burrows-Wheeler transform (BWT) using the
following example: T = GATTACA$. Also explain the reversibility of BWT.
[4 marks]
(d) Discuss the use of clustering in the analysis of gene expression microarray data.
[4 marks]
(e) Discuss the UPGMA algorithm as applied to the following distance matrix of
the species A, B, C and D.
species A B C
B 2
C 4 4
D 6 6 6
[4 marks]
