Exam for Advanced Bioinformatics - Part II Exam for Advanced ... - CBS

Exam for Advanced Bioinformatics - Part II Exam for Advanced Bioinformatics – Course 27614 Part II 7th of December 2004, Auditorium 51, building 208 The examination lasts 2 hours (9:00-11:00) and represents the second half of a two-part test. The two parts are evaluated jointly as pass/not pass. The exam is an open book exam so you can use • Any book • Pocket calculator • But no computers are allowed Students name: ___________________________________________________________ Student number: __________________________________________________________

Protein Modelling 1. What are the 7 structural classes as assigned by the DSSP program? ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________

Page 1 of 8

Exam for Advanced Bioinformatics - Part II 2. Explain short why BLOSUM encoded sequence representation works better than sparse encoding in neural network secondary structure prediction. Why is position specific scoring matrices even better and how do you obtain these. ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________

Page 2 of 8

Exam for Advanced Bioinformatics - Part II 3. Which grouping contains the most diverse set of sequences? a) Family b) Superfamily c) Fold Answer: _________

4. Describe the different kind of helices and their structural differences. ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________

Page 3 of 8

Exam for Advanced Bioinformatics - Part II 5. Describe the important steps in homology modelling ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________

Page 4 of 8

Exam for Advanced Bioinformatics - Part II

Sequence searching 6. Sequence weighting in Hidden markov models is used to a) Increase weight on heavy sequences b) To downweight sequences with many close homologues c) To upweight sequences with many close homologues Answer: _________

7. You run BLAST to identify the homologues of a protein. Which of the following 4 is the most reliable hit? a) E value = 0.1, % identical residues = 16 b) E value = 0.1, % identical residues = 30 c) E value = 0.001, % identical residues = 16 d) E value = 10, % identical residues = 16 Answer: _________

8. What is the information content in bits of a position with 95% serine and 5% alanine? Answer: _________

9. What is an epitope? ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________

Page 5 of 8

Exam for Advanced Bioinformatics - Part II

Microarray data analysis 10.

Why is it necessary to normalize microarray data? ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________

Page 6 of 8

Exam for Advanced Bioinformatics - Part II 11. Compare the assumptions that the different normalization methods are based on. ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________

Page 7 of 8

Exam for Advanced Bioinformatics - Part II 12. What is the principle of the two main types of clustering methods? Give two examples of how clustering can be applied to gene expression data from a microarray experiment. ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________

Page 8 of 8