Introduction to Bioinformatics (Fall 2002)
Questionnaire on notes: Genome Comparison
(please press SUBMIT button when finished)

I. Basic Information

A. Your name 
II. Problem Sets IntroM and IntroP
A. The authors of the articles claim that E. coli might have gained foreign DNA by viral infection. Do you understand how this might occur without killing the E. coli? 
B. Do you understand the principle behind a method that might distinguish DNA that E. coli recently acquired from DNA it shares with millions-of-years-worth of ancestors? 

C. Do you feel comfortable interpreting Tables 1 and 2? 

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

E. Two distantly related bacteria both have genes that encode the protein cytochrome c. The protein share considerable sequence similarity and probably shared a common ancestor perhaps a billion years ago. One of the bacteria also has two copies of the protein glutamine synthetase, each with slightly different functional properties than the other.

E.1. Which proteins are likely to be orthologs? 
E.2. Which proteins are likely to be paralogs? 
Comments for questions II.A through II.F:
III. Understanding the research article regarding genomic comparison
A. How comfortable do you feel reading the research article? 
B. How many captured viruses (prophages) are there in the pathogenic strain of E. coli described in the article you skimmed? I don't expect you to remember this from the article (if it ever entered your consciousness in the first place, but you should be able to find specific pieces of information of this sort in about half a minute. If it takes more than that, stop. We should discuss how to read articles nonlinearly, a very valuable skill. 
 
Comments for questions III.A and III.B:
IV. Design your class
A. Please choose up to three study questions that you would most like discussed in class:
SQ1 SQ2 SQ3 SQ4 SQ5 SQ6 SQ7
B. Put here any miscellaneous comments, questions, suggestions, concerns you may have. E.g., Progress in Perl? Problem sets too confusing? Don't know where we're going?
 

Thanks!

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