2008 Paper 8 Question 1
Bioinformatics
(a) Parameters of the positional independence of a transcription factor binding site
were estimated by the experimental positional nucleotide frequencies shown in
the following table:


1 2 3 4 5 6
T 0.16 0.05 0.01 0.03 0.12 0.14
C 0.08 0.04 0.01 0.03 0.05 0.11
A 0.68 0.11 0.02 0.90 0.16 0.51
G 0.08 0.80 0.96 0.04 0.67 0.24


Explain what a logo is and determine the parameters of the logo graph.
Compute the information content of one column. [8 marks]
(b) Discuss the complexity of the algorithm for finding a global alignment between
two DNA sequences that have a high degree of similarity. Present an example
and analyse it using the following scoring parameters: +1 for match, −1 for
mismatch, and d = −1 for a linear gap penalty. [7 marks]
(c) In modelling a metabolic process, describe the advantages and disadvantages
of using a stochastic approach (for example agents) as opposed to using a set
of deterministic differential equations. [5 marks]