Daily Dozen:
1. What are two reasons to do multiple alignment?
2. How is the distance measure defined?
3. What assumption does the sum-of-pairs score make? Is it justified?
4. Why are dynamic programming methods so slow with multiple sequence alignments?
5. What did Carillo and Lipman do to make dynamic programming feasible?
6. Why "once a gap, always a gap"?
7. What are some of the heuristics that CLUSTAL W used to improve its performance?
8. What are some common problems with progressive alignment algorithms?
9. Explain the concept of iterative alignment.
10. At what sequence identity do we begin to see structural similarity?
11. Why does a HMM MSA start off with high indel penalties?
12. Can you think of any biological reason why proteins would align better forward vs backward? (I can't)
1. What are two reasons to do multiple alignment?
2. How is the distance measure defined?
3. What assumption does the sum-of-pairs score make? Is it justified?
4. Why are dynamic programming methods so slow with multiple sequence alignments?
5. What did Carillo and Lipman do to make dynamic programming feasible?
6. Why "once a gap, always a gap"?
7. What are some of the heuristics that CLUSTAL W used to improve its performance?
8. What are some common problems with progressive alignment algorithms?
9. Explain the concept of iterative alignment.
10. At what sequence identity do we begin to see structural similarity?
11. Why does a HMM MSA start off with high indel penalties?
12. Can you think of any biological reason why proteins would align better forward vs backward? (I can't)