Discuss with one example how the stiffness parameter affects soft k-means clustering
Describe the time and space complexity for finding the global alignment between two DNA sequences when they are very similar
March 21, 2023Describe Ruth Nussinov’s algorithm on RNA folding and its complexity
March 21, 2023Discuss with one example how the stiffness parameter affects soft k-means clustering
COMPUTER SCIENCE TRIPOS Part II – 2020 – Paper 9
Bioinformatics (pl219)
(a) You are given a table of gene expression data. Each row corresponds to a gene
and in the columns there is the gene expresson at different time steps (or different
experimental conditions). Discuss at least one method, with one example, to
identify genes with similar behaviour in time and the method’s complexity and
limitations. [4 marks]
(b) Discuss with one example how the stiffness parameter affects soft k-means
clustering. [4 marks]
(c) Describe the advantage of using suffix arrays to find matches in genome
sequencing. [4 marks]
(d) Describe solutions to the problem of ‘bubbles’ in De Bruijn graphs of genomes.
[4 marks]
(e) Describe opportunities and challenges presented by DNA storage of data
including a technique for indexed retrieval. [4 marks]
