Introduction to Bioinformatics (Fall 2002)
Questionnaire on notes: Progress, Scoring, Protein alignment
(please press SUBMIT button when finished)

I. Basic Information

A. Your name 
II. Progress in Scenario 3
A. Whether or not you know how to solve the mystery, do you at least see how it has evolved? 
B. Whether or not you know how to make the specific changes, do you at least see where and more or less how you might alter the local BlastN program to print out scoring matrices? 

C. How comfortable are you in making minor changes in programs? 

D. Out of curiosity, when you go through the notes, is it your habit to actually run the example programs? 
 
Comments for questions II.A through II.D:
III. Evaluating significance of scores
A. How comfortable are you with the explanation behind equation 1 in the notes, i.e. how to calculate the expected number of exact matches between two sequences? 
B. Can you find in Blast output (from the web) the E-value, raw score, and bits score? 

C. How comfortable are you with the relationship between these three quantities? 

 
Comments for questions III.A through II.C:
IV. Protein alignments
A. How comfortable are you with reading a PAM frequency table (e.g. Table 2) and a log odds table (e.g. Fig. 3)? 
B. How comfortable are you with the distinctions between the different versions of PAM and between the different versions of BLOSUM? 

C. How comfortable are you calculating the score of an amino acid alignment? 

 
Comments for questions IV.A through II.C:


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 SQ7 SQ8 SQ9 SQ10
B. Put here any miscellaneous comments, questions, suggestions, concerns you may have. Tell us what you need.
 

Thanks!

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