Daily Dozen:
1. What should you think about when picking a scoring matrix for your alignment?
2. What evolutionary distance does PAM35 represent?
3. We often use PAM250, whether it's appropriate or not. How will this affect our alignments?
4. Why do the higher-numbered PAM matrices have a higher chance of error?
5. PAM matrices are based on Markov models, which assume that each amino acid is independent of the previous. Is this appropriate? Why does it work anyway?
6. How do you know when you've chosen the correct PAM matrix? Is this a good way to decide when your proteins diverged?
7. Explain amino acid mutability.
8. Where did the BLOSUM matrices come from?
9. What assumptions are made when using the BLOSUM matrices?
10. When would you use a BLOSUM30 vs a BLOSUM62 matrix?
11. What is an affine gap penalty?
12. What are two ways to assess scores for global alignments?
1. What should you think about when picking a scoring matrix for your alignment?
2. What evolutionary distance does PAM35 represent?
3. We often use PAM250, whether it's appropriate or not. How will this affect our alignments?
4. Why do the higher-numbered PAM matrices have a higher chance of error?
5. PAM matrices are based on Markov models, which assume that each amino acid is independent of the previous. Is this appropriate? Why does it work anyway?
6. How do you know when you've chosen the correct PAM matrix? Is this a good way to decide when your proteins diverged?
7. Explain amino acid mutability.
8. Where did the BLOSUM matrices come from?
9. What assumptions are made when using the BLOSUM matrices?
10. When would you use a BLOSUM30 vs a BLOSUM62 matrix?
11. What is an affine gap penalty?
12. What are two ways to assess scores for global alignments?