BNFO 301 
Introduction to Bioinformatics
Questionnaire on: Repeats, Tandem Repeats, and Pattern Matching
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(If you encounter a question you've answered in a previous questionnaire and nothing has changed, just skip over it)
Spring 2014 


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?
III. Repeated Sequences
  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?
IV. Tandem Repeated Sequences
  1. What understanding do you have of Southern Blots?
  2. What understanding do you have of how Southern Blots can be used to detect repeated sequences?
  3. Were you able to get and understand the GenBank file of the cpeBA region of Calothrix PCC 7601?
  4. What progress have you made in making a homemade annotation of the cpeBA region?
  5. 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?
  6. What sense do you make of Mazel et al's Fig. 1?

     
  7. Do you have any favorite study questions (SQ1-SQ13) you think need discussion?
V. Pattern Matching
  1. Were you able to find instances of the STRR1 unit in the cpeBA region? If not, were you blocked by any conceptual problems?
  2. Were you able to use the {n,} specification to find repeats? Do you understand how it works?
  3. Were you able to use the `1 specification to find repeats? Do you understand how it works?
  4. Do you understand why both methods are limited in their ability to find inexact repeated sequences where the pattern is not already known?

     
  5. Do you have any favorite study questions (SQ14-SQ21) you think need discussion?
VI. Miscellaneous
Any other comments, questions, suggestions, or concerns you may have?

Thanks!

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