BNFO 301
Introduction to Bioinformatics
Questionnaire on: Finding DNA Regulatory Sequences
(please press SUBMIT button when finished)
Spring 2006

I. Basic Information

A. Your name 
II. Models of Regulation
A. How comfortable are you with the notion that an organism might find advantage in regulating the expression of gene (for example the lac operon)? 

B. How comfortable are you with the notion that genes may be regulated by a negatively-acting regulatory protein, a repressor (for example the Lac repressor)? 

C. How comfortable are you with the notion that genes may be regulated by a positive-acting regulatory protein (for example CRP)? 

D. How comfortable are you with the central role of RNA polymerase and the significance of a promoter ? 

E. How comfortable are you with the significance of dimeric DNA-binding proteins and palindromic binding sites? 

F. How comfortable are you with how gene regulation differs between eukaryotes and bacteria? 

G. Choose a study question if you want it discussed in class:

     SQ1 SQ2 SQ3 SQ4
 
Comments re
regulatory DNA

III. Position-specific scoring matrices
A. Do you see why searching for consensus sequences is not generally an effective way to find regulatory sequences? 

B. How comfortable are you with interpretting the alignment shown in Fig. 5? 

C. How comfortable are you in calculating a Table of occurrences (Table I.B), given a set of aligned sequences? 

D. How comfortable are you in calculating a PSSM (Table I.C), given a set of aligned sequences? 

E. How comfortable are you in using a PSSM to score a given sequence (Table II)? 

F. How comfortable are you with the need for pseudocounts?  

G. How comfortable are you with the calculation of pseudocounts?  

H. Choose up to four study questions that you would most like discussed in class:

     SQ5 SQ6 SQ7 SQ8 SQ9 SQ10 SQ11 SQ12 SQ13 SQ14 SQ15 SQ16 SQ17 SQ18
 
Comments re
PSSMs

IV. Miscellaneous
A. I just asked you lots of questions through the extensive questionnaire attached to the exam, and I'm still far from digesting all you had to say.
    So I'll give you a pass on the usual "How are things going?"
 
(...unless you have 
something you want to say)

 
Thanks!
  REMEMBER TO CLICK SUBMIT! (or click RESET to start over)