+University College Dublin An Coliste Ollscoile Baile tha Cliath

SEMESTER 2 EXAMINATION 2010/2011

COMP 40400 Bioinformatics

Prof. M. McGinnity Prof. J. Carthy Dr. Gianluca Pollastri

Time allowed: 2 hours Instructions for candidates Answer any three questions. All questions carry equal marks. The paper is marked out of 100. Use of calculators is prohibited. Instructions for invigilators Use of calculators is prohibited.

UCD 2010/11/Modular

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Answer any three of the following 4 questions. (33 marks each + 1 mark bona fide) 1) Given the 2 sequences: CCCATGCCATGAC ATGCGTGTC a) Build the matrix of maximal similarity between them according to the SmithWaterman algorithm (local alignment), using the scores: match=1; mismatch=-1; gap= -3. (23 marks) b) Extract the optimal alignment in downmost fashion from the matrix. (10 marks)

2) a) What is protein secondary structure, and why would one want to predict it? (10 marks) b) Discuss the prediction of protein secondary structure, in particular by machine learning methods. (15 marks) c) For which type of protein structure prediction (homology modelling or ab initio) would you think that good secondary structure predictions would be most useful? Discuss why. (8 marks)

3) a) Describe the Neighbour Joining method for phylogeny reconstruction. (10 marks) b) Describe Maximum Parsimony methods for phylogeny reconstruction. (10 marks) c) Discuss the main points of contact between these two classes of methods, but also the main differences. What is the main product of Maximum Parsimony methods that Neighbour Joining cannot provide? What is the main disadvantage of Maximum Parsimony vs. Neighbour Joining? (13 marks)

4) a) Discuss the main general differences between template-based methods (a.k.a. homology modelling, or comparative modelling), and template-free methods (a.k.a. ab initio or de novo) for protein structure prediction. (10 marks) b) Could you sketch a basic pipeline for template-based prediction? Which of its elements would be missing in a template-free pipeline? (10 marks) c) Can you discuss the role of algorithms for sequence comparison in the context of protein structure prediction (template-based, and template-free)? (13 marks)

UCD 2010/11/Modular

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