BNFO 301 
Introduction to Bioinformatics
Questionnaire on Genome Analysis - Sequence Contrasts (dinucleotide/codon 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. 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 

C. 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 (both Wednesday's and Monday's notes)
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 from Wednesday's notes that you would most like discussed in class:

SQ11  SQ12  SQ13  SQ14 

B. Choose study questions from Monday's notes that you would most like discussed in class:

SQ1  SQ2  SQ3  SQ4  SQ5  SQ6  SQ7  SQ8 
(note: SQ9 was excluded because we have not discussed the BioBIKE concept of 'tables',
without which you'd be hard pressed to answer this question)

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

  • Why might codon frequencies hold reasonably constant for genes of a specific genome?
  • Why is calculating codon frequencies more complicated (I don't mean more tedious) than calculating dinucleotide frequencies?
  • What is the distinction between absolute and relative codon frequencies?
  • Do you feel able to calculate a relative codon frequency, given the data in the table on page 2 of the notes?
  • Does the calculation of relative codon frequency shown at the top of Box 3 make sense?
     
V. Meta-questions
A. Put here any miscellaneous comments, questions, suggestions, concerns you may have.
 

Thanks!

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