Introduction to Bioinformatics (Fall 2003)
Questionnaire on notes: Sequence Alignment
(please press SUBMIT button when finished)

I. Basic Information

A. Your name 
II. Problem Sets IntroM and IntroP
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?
C. How comfortable are you in filling out a scoring table?

D. Do you understand the notion of word-searching as done by Blast? 

E. Do you see the mechanism by which Blast is able to run much faster than the Smith-Waterman algorithm? 

F. Do you understand how filtering the query sequence can alter the matches that are found?

G. Do you have an explanation for the mystery outlined in Scenario 3? 
 
Comments for questions II.A through II.G:

V. Design your class
A. Please choose up to four study questions that you would most like discussed in class:
SQ1 SQ2 SQ3 SQ4 SQ5 SQ6 SQ7SQ8
B. Put here any miscellaneous comments, questions, suggestions, concerns you may have. E.g., You'd like to go over question X of the exam.
 

Thanks!

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