Integrated Bioinformatics(Fall 2004)
Questionnaire on notes:Genome Comparison
(please press SUBMIT buttonwhen finished)

I. Basic Information

A. Your name 
II. Genome comparison
A. The authors ofthe articles claim that E. coli might have gained foreign DNA byviral infection. Do you understand how this might occur without killingthe E. coli
B. Do you understandthe principle behind a method that might distinguish DNA that E. colirecently acquired from DNA it shares with millions-of-years-worth ofancestors? 

C. Do you feel comfortableinterpreting Tables 1 and 2? 

D. Which of the two mutationsin codons below would result in a change in the amino acid sequence ofthe encoded protein?

E. Two distantly relatedbacteria both have genes that encode the protein cytochrome c. The proteinshare considerable sequence similarity and probably shared a common ancestorperhaps a billion years ago. One of the bacteria also has two copies ofthe protein glutamine synthetase, each with slightly different functionalproperties than the other.

E.1. Which proteinsare likely to be orthologs? 
E.2. Which proteins arelikely to be paralogs? 
Comments for questions II.Athrough II.F:
III. Understanding the researcharticle regarding genomic comparison
A. How comfortabledo you feel reading the research article? 
B. How many capturedviruses (prophages) are there in the pathogenic strain of E. coli describedin the article you skimmed? I don't expect you to remember this from thearticle (if it ever entered your consciousness in the first place), butyou should be able to find specific pieces of information of this sortin about half a minute. If it takes more than that, stop. We should discusshow to read articles nonlinearly, a very valuable skill. 
 
What would you need to knowto reach a satisfying understanding of your article? Other comments forquestions III.A and III.B?
IV. Design your class
A. Please chooseup to three study questions that you would most like discussed in class:
SQ1 SQ2 SQ3 SQ4 SQ5 SQ6 SQ7
B. Put here anymiscellaneous comments, questions, suggestions, concerns you may have.E.g., Progress in Perl? Don't know where we're going?
 

Thanks!

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