Questions for graduate students are bonus questions for others!
- What is dynamic programming? Give one example for its use in bioinformatics.
- How old is planet Earth?
- How old are the oldest sedimentary rocks?
- What is a Snowball Earth event?
- How old (approximately) is the Universe according to the Big Bang Scenario?
- A pairwise sequence alignment calculated with the Needleman-Wunch algorithm is the best possible alignment given the parameters (scoring matrix, gap penalty).
A) this alignment is always better in aligning homologous structures than a multiple sequence alignment
B) The Needleman-Wunch algorithm provides the single best alignment.
C) The alignment is optimal (as measured by the alignment score), but there might be many equally optimal pathways/traces through the scoring table.
- What are the three steps clustal performs to align sequences?
- Which biomolecule was first used to place microorganisms onto the tree of life?
- Offspring that is similar to its parents and the creation of variation is necessary for evolution by natural selection to occur. One way for the variation to occur is through random point mutation. What other processes do or could occur?
- Are any of the processes that you listed in question 9 a violation of the Darwinian theory of natural selection? Give a one sentence explanation of your reasoning.
- According to the currently favored version of the tree of life, which prokaryotic domain is the closest relative of the nucleocytoplasm?
- Which organism have primary plastids, i.e. plastids that evolved directly from a cyanobacterial endosymbiont?
- List at least three groups of organisms that have secondary plastids, i.e. plastids that evolved form a secondary endosymbiosis with a eukaryotic algae.
- What process is called transcription, and what enzymes perform it?
- What process is called translation, and what enzymes perform it?
- What process is called replication, and what enzymes perform it?
- What advantages does a command line interface have over a graphics user interface?
- The following diagram gives the relation between the number of substitutions that have occurred during evolution (x axis) and the observed fraction of sequence differences. The depicted curve corresponds to the Jukes Cantor correction for a nucleotide sequence. This correction is only correct, if all sites have the same probability to undergo a substitution, and if all nucleotides occur with the same frequency.
Provide a rough sketch of how this relationship would change if the different sites would have different substitution frequencies, and some sites would only very rarely undergo a substitution.
- In the above diagram (use a different color) indicate how the curve would change, if the sequences were actually aligned by an alignment program.
- Given two sequences ATTACAG and ACTAAG draw and fill in the matrix that an alignment algorithm using dynamic programming would use. Assume a gap penalty of x*0.1+.9, where x is the size of the gap, a positive score of 10 for identity, 1 for a transition, 0 for a transversion.
What is the optimal score for this alignmet?
Which alignment(s) correspond(s) to this score?
- How does a region of low complexity look in dotlet?
- Draw a diagram of how a sequence comparison in dotlet would look like between two sequences (seq1 on the x axis), where sequence sequence 2 is homologous to sequence 1, but has a large deletion.
- How would an internal duplication in sequence 1 look in dotlet?
- The lengths of introns is not always a multiple of 3, and therefore neighboring exons are not always in the same reading frame. For alternative splicing to work, do the exons need to be in the same reading frame?
For graduate students (extra point for undergraduates)
- How can the ATPases help to find the root in the tree of life?
- Does natural selection depend to the presence of a biopolymer that can be replicated? Explain your answer.