BNFO 301
Introduction to Bioinformatics
Questionnaire on: Sequence-contrasts (Part II)
(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. Dinucleotide biases

A. How comfortable are you with counting dinucleotides in a genome? 

B. How comfortable are you calculating dinucleotide frequencies? 

C. Do you see the overlap between the information inherent in dinucleotide frequencies and in GC-fraction? 

D. Do you see why the dinucleotide bias calculation described in the notes dissociates the information in dinucleotides from the information in mononucleotides? 

E. How comfortable are you with the calculation of dinucleotide bias as shown in Box 2? 

F. How comfortable are you in calculating dinucleotide biases within BioBIKE? 

Comments re
Calculation of
dinucleotide biases:
III. Dinucleotide bias comparisons

A. How comfortable are you with the calculation on the right side of Box 2, comparing two sets of dinucleotide biases? 

B. How comfortable are you calculating a comparison of biases within BioBIKE? 

Comments re
Comparison of
biases:
IV. Codon usage
The notes were intended to provide a preliminary greeting to codon usage.

A. How comfortable are you with the ideas involved in codon usage so far? 

Comments re
Codon usage:
V. 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 
SQ10  SQ11  SQ12  SQ13  SQ14 
VI. 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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