BNFO 301 
Introduction to Bioinformatics
Questionnaire on Genome Analysis - Sequence Contrasts (dinucleotide frequencies)
(please press SUBMIT button when finished)
(and please don't use quotation marks in your answers. They break the questionnaire program!)
Spring 2009 

I. Basic Information

A. Your name 
II. Sequence contrasts - GC content

A. How far have you gotten in the tour concerning GC content?  

C. Choose study questions that you would most like discussed in class:

SQ1  SQ2  SQ3  SQ4  SQ5  SQ6  SQ7  SQ8  SQ9 
SQ10  SQ11  SQ12  SQ13  SQ14  SQ15  SQ16  SQ17 

Comments, questions, concerns regarding Karlin's article and GC content?
     

III. Dinucleotide biases

A. How far have you gotten in the tour concerning dinucleotide frequencies?  

B. Choose study questions that you would most like discussed in class:

SQ1  SQ2  SQ3  SQ4  SQ5 
SQ6  SQ7  SQ8  SQ9  SQ10 

Perhaps the following will inspire you to comment in the box below:

  • Calculation of dinucleotide biases
    • Counting dinucleotides in a genome?
    • Calculating dinucleotide frequencies?
    • Overlap between the information inherent in dinucleotide frequencies and in GC-fraction?
    • Why the dinucleotide bias calculation described in the notes dissociates the information in dinucleotides from the information in mononucleotides?
    • Calculation of dinucleotide bias as shown in Box 2?
    • Calculating dinucleotide biases within BioBIKE?
  • Comparison of dinucleotide biases
    • The calculation on the right side of Box 2, comparing two sets of dinucleotide biases?
    • Calculating a comparison of biases within BioBIKE?
     
IV. Codon usage
The notes were intended to provide a preliminary greeting to codon usage. If you didn't get this far, not to worry.

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

SQ11  SQ12  SQ13  SQ14 

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

Comments re
Codon usage:
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?
    What did you think about the session with the high school people?
 

Thanks!

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