BNFO 301 
Introduction to Bioinformatics
Questionnaire on: Local repeats and finding them / Pattern matching
(please press SUBMIT button when finished)
(If you encounter a question you've answered in a previous questionnaire and nothing has changed, just skip over it)
Spring 2015 


I. Basic Information

A. Your name 
II. Old Business
  1. Any final concerns about Gene Regulation and Bacteriophages?

     
  2. Any final concerns about Search for Regulatory Sequences?
    (e.g.
    • How MOTIFS-IN works?
    • How to understand the output of MOTIFS-IN?
    • How to use it to find regulatory sequences?

     
  3. Any final concerns about Problem Set 5 or Problem Set 6?

     
  4. Any initial comments or concerns you have regarding your group's topic?
    Your efforts to find an individual topic?
    Or anything else related to the research project?
III. Repeated Sequences, Tandem Repeats, and Pattern Matching
  1. How far did you get in the tour Repeats, Tandem Repeats, and Pattern Matching?

     
  2. Do you understand why searching for repeated sequences might be rewarding?
  3. Do you understand the different types of repeated sequences?

    Tandem Repeats
     
  4. What understanding do you have of Southern Blots?
  5. What understanding do you have of how Southern Blots can be used to detect repeated sequences?
  6. Were you able to get and understand the GenBank file of the cpeBA region of Calothrix PCC 7601?
  7. What progress have you made in making a homemade annotation of the cpeBA region?
  8. What understanding do you have of the purpose of the restriction enzyme XbaI in producing the blot shown in Mazel et al's Fig. 1?
  9. What sense do you make of Mazel et al's Fig. 1?

     
  10. Do you have any favorite study questions (SQ1-SQ13) you think need discussion?

    Pattern Matching
     
  11. Were you able to find instances of the STRR1 unit in the cpeBA region? If not, were you blocked by any conceptual problems?
  12. Were you able to use the {n,} specification to find repeats? Do you understand how it works?
  13. Were you able to use the `1 specification to find repeats? Do you understand how it works?
  14. Do you understand why both methods are limited in their ability to find inexact repeated sequences where the pattern is not already known?

     
  15. Do you have any favorite study questions (SQ14-SQ21) you think need discussion?
IV. Finding Local Repeats - Dot Plots
  1. How far did you get in the tour Finding Local Repeats?

     

    Dot Plots
     
  2. Do you know how to interpret dot plots?
  3. Do you understand how dot plots may be used to detect repeated sequences?
  4. Can you imagine how dot plots work (the algorithm)?
  5. Do you have any favorite study questions (SQ1-SQ10) you think need discussion?

    Autocorrelation
     
  6. What understanding do you have of the conceptual algorithm underlying autocorrelation?
  7. What understanding do you have of how to interpret the output of the autocorrelation function?
  8. What understanding do you have of how the implementation works (the code)?

     
  9. Do you have any favorite study questions (SQ11-SQ22) you think need discussion?
V. Miscellaneous
Any other comments, questions, suggestions, or concerns you may have?

Thanks!

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