TU Wien:Bioinformatik VO (Mach)/Prüfung 2014-02-06

1. Characterize how information is stored in DNA-, RNA-, and protein sequences? Beside sequence information, what additional information is important for RNA und protein molecules?
2. Explain global vs. local alighment by simple diagrams.
3. Prepare a dataplot matrix for sequences A: atggctg and B: atggctgatatggctg (coding: corresponding of letters = 1, all other cases = 0, highlight diagonales, and derive alignment)
4. Calculate the Levensthein distance by using the Needleman-Wunsch algorithm for the sequences A := atgcaat, B := atgct and applying an n times m matrix and the principle of "dynamic programming". (Initialize the matrix with 2,4,6,8,10,12,... for introducing only gaps; gap = 2, correspondence between letters = 0, non-correspondence between letters = 1). Derive also the alignment form the matrix.
5. What is the difference between a motive and a pattern search in a peptide?
6. What is KEGG, name at least 5 KEGG databases.
7. What is comparative genomcis; explain the theoretical background and give an example?
8. What is evolution? Explain using "gene frequency" term?
9. What is the law of parsimony?
10. Why JC69 is considered to be the most constrained model of evolution?