Daily Dozen:
1. Can you think of some more reasons why you would want to align a sequence to a database?
2. What types of databases are available?
3. What is a k-tuple?
4. What is the sequence complexity of AAAAAAAAAAAA? How about ACTGACTGACTG? Why is it important to calculate sequence complexity in windows?
5. What is a finite state machine?
6. What's an MSP?
7. How does requiring two neighboring hits to spark an extension reduce the number of extensions?
8. What are some BLAST parameters and what do they do? e.g. wordsize, threshold, etc.
9. How does MegaBlast achieve such a speedup? What are some potential problems of this approach?
1. Can you think of some more reasons why you would want to align a sequence to a database?
2. What types of databases are available?
3. What is a k-tuple?
4. What is the sequence complexity of AAAAAAAAAAAA? How about ACTGACTGACTG? Why is it important to calculate sequence complexity in windows?
5. What is a finite state machine?
6. What's an MSP?
7. How does requiring two neighboring hits to spark an extension reduce the number of extensions?
8. What are some BLAST parameters and what do they do? e.g. wordsize, threshold, etc.
9. How does MegaBlast achieve such a speedup? What are some potential problems of this approach?