How can you be reasonably confident that an amino acid multiple sequence alignment is optimal?
Describe the differences in complexity and usage between hierarchical clustering and the Markov clustering (MCL) algorithm
March 21, 2023Given the two DNA sequences: GCACTT and CCCAAT
March 21, 2023How can you be reasonably confident that an amino acid multiple sequence alignment is optimal?
COMPUTER SCIENCE TRIPOS Part II – 2014 – Paper 9
Bioinformatics (PL)
(a) How can you be reasonably confident that an amino acid multiple sequence
alignment is optimal? [6 marks]
(b) From gene expression analysis we hypothesize that each DNA sequence of a
dataset from a different animal species contains at least one similar short
subsequence at an unknown position in the dataset. Explain the procedure
to identify the short subsequence in the dataset and then cluster the species
according to the similarity of the short subsequence. [8 marks]
(c) Which algorithms might be useful in aligning very long DNA sequences, such as
entire genomes and why? [6 marks]
