BNFO 301 
Introduction to Bioinformatics
Questionnaire on: Finding Local Repeats
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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 Search for Regulatory Sequences and MOTIFS-IN?

     
  2. Any final concerns about Repeats, Tandem Repeats, and Pattern Matching?
    (e.g.
    • How Southern blots works?
    • What tandem repeats look like in at least one natural genome?
    • How to use the {n,} specification of MATCHES-OF-PATTERN to find tandem repeats?
    • How to use the `1 specification of MATCHES-OF-PATTERN to find tandem repeats?)
III. Finding Local Repeats - Dot Plots
  1. How far did you get in the tour Finding Local Repeats?

     
  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?
IV. Finding Local Repeats - Autocorrelation
  1. What understanding do you have of the conceptual algorithm underlying autocorrelation?
  2. What understanding do you have of how to interpret the output of the autocorrelation function?
  3. What understanding do you have of how the implementation works (the code)?

     
  4. Do you have any favorite study questions (SQ11-SQ22) you think need discussion?
V. Research Project
Any initial comments or concerns you have regarding your group's topic?
Or anything else related to the research project?
VI. Miscellaneous
Any other comments, questions, suggestions, or concerns you may have?

Thanks!

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