I. Basic Information

A. Your name 

A. Using the given parameters, calculate the local alignment score of the alignment below: 

Match reward = +1        Mismatch penalty = -2        Gap opening penalty = -3        Gap extension penalty = -2

GAGAC--CTAGAAC
  |||  |||| ||
CTGACGGCTAGTAC

B. How comfortable are you in calculating alignment scores? Select Very comfortable Moderately comfortable Somewhat comfortable Not comfortable

C. How comfortable are you in filling out a scoring table? Select Very comfortable Moderately comfortable Somewhat comfortable Not comfortable

D. Do you understand the notion of word-searching as done by Blast?  Select  Yes  No 

E. Do you see the mechanism by which Blast is able to run much faster than the Smith-Waterman algorithm?  Select  Yes  No 

F. Do you understand how filtering the query sequence can alter the matches that are found? Select  Yes  No 

G. Do you have an explanation for the mystery outlined in Scenario 3?  Select  Yes  No 

H. Please choose up to four study questions that you would most like discussed in class:

SQ1 SQ2 SQ3 SQ4 SQ5 SQ6 SQ7SQ8
 

Comments for questions II.A through II.G:

III. Miscellaneous

A. Your thoughts on the recent exam experience? Any questions you'd particularly like to go over?  
B. Put here any miscellaneous comments, questions, suggestions, concerns you may have.  

Thanks!

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