Homework 2 - BLAST

Part 1: 

1. The nr database is "non-redundant". This is advantageous for a number of 
   reasons, almost all of which is due to the fact that this is a smaller
   database file than if you had just blindly combined Swiss-PROT, GenBank,
   and the model organism databases. The smaller size is good for computational
   reasons as BLAST can run faster. It's good for statisitical reasons because
   the smaller database means that you would expect to see fewer hits with a 
   high score. It's also good for biological reasons because in many cases two
   labs have sequenced the same gene and given it two different names. The nr
   database will hopefully prevent confusion caused by this.

2. 40

3. Saccharomyces castelli

4. Score 808 bits, %identity = 52%.

5. I got 39 hits with an e-value < 1.   This is less than before, 
   this is because we changed the matrix and are using blosum80 which looks for more 
   identity because the matrix was formed from proteins with at least 80% identity.
   The blast is therefore more stringent because the aligments have to be better in 
   order to score well.  This matrix is better than blosum62 for differentiating between
   closely related sequences.

6. Saccharomyces dairenensis

7. Score = 825 bits, ID = 66%

8. 46 hits, less than before. This might be two to two reasons:
   1: The extension penalty was increased, so long gaps incur a higher penalty, resulting in 
      a lower number of hits.
   2: We have decresed the penalty for small gaps, so many more hits will score well. This 
      increases the statistical threshold needed for a statistically significant hit, resulting
      in fewer significant hits.
9. The score is lower. This is due to the fact that BLAST has now inserted more gaps. And the 
   gap extension score is larger.

10. This will likely take longer. Lowering the word size means more hits will be found 
    initially, meaning more sequence that need to be extended and joined together. Making more
    work for blast. 


Part 2: Your favorite gene was part of the 

see my example code. I also posted code from a student in the class who solved the problem
slightly differently than I did. Hopefully showing you that there are many, many different
ways to tackle a programming problem.