Introduction to Bioinformatics (Fall 2003)
Questionnaire on notes: Position-specific scoring matrices
(please press SUBMIT button when finished)

I. Basic Information

A. Your name 
II. Nature of PSSMs
A. How comfortable are you with the basic principles behind constructing PSSMs? For example, could you have made Table 1B (Table of occurrences) yourself? 

B. How comfortable are you about going from a table of occurences to a frequency table? For example, could you have made Table 1C yourself? 

C. How comfortable are you about using a PSSM to score a sequence? For example, could you have determined the values in the line marked "Score" of Table 2? (Never mind pseudocounts for the moment) 
Comments for questions II.A through II.C:

III. Adjustments to PSSMs
A. How comfortable are you with the notion of pseudocounts in the calculation of PSSMs? Could you do such a calculation yourself? 

B. How comfortable are you with the notion of normalization with respect to overall nucleotide frequencies? Could you do such a calculation yourself? 

C. How comfortable are you with the meaning and calculation of uncertainty and information content? 
Comments for questions III.A through III.C:

IV. Miscellaneous
A. Please choose up to four study questions from the notes 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.

 

Thanks!

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