Compare the use of the affine gap penalty with the constant gap penalty
Describe a bioinformatics application of hidden Markov models
March 21, 2023Hidden Markov models (HMM) are widely used in Bioinformatics
March 21, 2023Compare the use of the affine gap penalty with the constant gap penalty
2006 Paper 8 Question 13
Bioinformatics
(a) Why do we use dynamic programming algorithms for pairwise sequence
alignment problems but not for multiple pairwise alignment? [5 marks]
(b) Compare the use of the affine gap penalty with the constant gap penalty.
[3 marks]
(c) Discuss the properties and assumptions of the Jukes–Cantor and the Kimura
2-parameter models of DNA evolution. [5 marks]
(d) Describe the UPGMA algorithm. [4 marks]
(e) What does the ultrametric property of a tree tell us about the evolutionary
process? [3 marks]
