BNFO 301
Introduction to Bioinformatics
Questionnaire on: Sequence-contrasts (Part III)
(please press SUBMIT button when finished)
Spring 2008

I. Basic Information

A. Your name 

B. Have you responded to the Special Questionnaire posted Monday, March 17? (If so, thanks) (If not, please do)

C. How far did you get in the notes? 

II. Codon biases

A. Do you see why codon frequencies might hold reasonably constant for genes of a specific genome? 

B. Do you understand why calculating codon frequencies is more complicated (I don't mean more tedious) than calculating dinucleotide frequencies? 

C. Do you understand the distinction between absolute and relative codon frequencies? 

D. How comfortable are you calculating a relative codon frequency given the data in the table on page 2 of the notes? 

E. How comfortable are you with the calculation of relative codon frequency as shown at the top of Box 3? 

Comments re
Calculation of
codon frequency:
III. Dinucleotide bias comparisons

A. How comfortable are you with the steps required to compare the codon frequencies of two organisms for the codons of a single amino acid? 

B. How comfortable are you with the second expression in Box 3? 

C. What problems have you encountered in translating the outline of the codon bias calculation into BioBIKE code? (answer below)

Comments re
codon bias
IV. The whole thing

A. Choose up to five study questions that you would most like discussed in class:

SQ1  SQ2  SQ3  SQ4  SQ5  SQ6  SQ7  SQ8  SQ9 
V. Meta-questions
A. Put here any miscellaneous comments, questions, suggestions, concerns you may have.
    For example, loops and maps getting any clearer? DEFINE-FUNCTION?
 

Thanks!

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