Introduction to Bioinformatics (Fall 2003)
Questionnaire on notes: Detection of anomalous regions of a genome
(please press SUBMIT button when finished)

I. Basic Information

A. Your name 
II. Old business
 
How far are you/we along in reaching a satisfactory conclusion to Scenario 7 (threading UDP glucose dehydrogenase)? What would you like to see done on Monday?

III. Prehistory: Pathogenicity islands and G+C fraction

A. How comfortable are you with the notion of pathogenicity islands -- how they arose and how they relate to pathogenicity? 

B. Do you see how measuring local G+C content can (at least sometimes) detect pathogenicity islands? 

C. Do you understand what problems may prevent the method of G+C content from being generally successful in detecting pathogenicity islands? 
 
Comments for questions III.A through II.C:

IV. Genome signature contrasts (dinucleotide frequencies) and codon bias
A. Can you make sense out of Karlin (2001)? 

B. Do you understand what the analysis of genome signature contrasts is trying to accomplish? 

C. How comfortable are you in calculating the relative abundance of a specific dinucleotide (rho*XY)? 

D. How comfortable are you in calculating the difference between signature profiles (delta*(f,g)?

E. Do you understand why codon usage might be useful in detecting pathogenicity islands? 

F. How comfortable are you in calculating the bias in codon usage of one set of genes relative to another (B(F|G))? 
 
Comments for question IV.A through IV.F:

V. Detection of individual alien genes
A. Do you see how Mrazek et al applied codon bias to the detection of individual alien genes? 

B. Do you have an idea how Markov analysis achieved its literary goals? 
 
Comments for question V.A through V.B:

Miscellaneous
A. Please choose study questions from the notes that you would most like discussed in class:
SQ1 SQ2 SQ3 SQ4 SQ5 SQ6
B. Put here any miscellaneous comments, questions, suggestions, concerns you may have.
 

Thanks!

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