TU Wien:Bioinformatik VO (Mach)/Prüfung 2014-02-06
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- Characterize how information is stored in DNA-, RNA-, and protein sequences? Beside sequence information, what additional information is important for RNA und protein molecules?
- Explain global vs. local alighment by simple diagrams.
- 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)
- 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.
- What is the difference between a motive and a pattern search in a peptide?
- What is KEGG, name at least 5 KEGG databases.
- What is comparative genomcis; explain the theoretical background and give an example?
- What is evolution? Explain using "gene frequency" term?
- What is the law of parsimony?
- Why JC69 is considered to be the most constrained model of evolution?